diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6489772..20bd530 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -14,15 +14,13 @@ jobs:
 
       - uses: actions/setup-go@v5
         with:
-          go-version: '1.24'
+          go-version: '1.26'
 
       - name: Download dependencies
         run: go mod download
 
       - name: Run tests
-        # Note: -race disabled due to pre-existing race conditions in tests that spawn
-        # background goroutines. These should be fixed by adding proper synchronization.
-        run: go test -v ./...
+        run: go test -race -v ./...
 
   lint:
     runs-on: ubuntu-latest
@@ -31,12 +29,12 @@ jobs:
 
       - uses: actions/setup-go@v5
         with:
-          go-version: '1.24'
+          go-version: '1.26'
 
       - name: golangci-lint
-        uses: golangci/golangci-lint-action@v6
+        uses: golangci/golangci-lint-action@v7
         with:
-          version: latest
+          version: v2.9.0
 
   security:
     runs-on: ubuntu-latest
@@ -45,16 +43,20 @@ jobs:
 
       - uses: actions/setup-go@v5
         with:
-          go-version: '1.24'
+          go-version: '1.26'
+
+      - name: Install gosec
+        run: go install github.com/securego/gosec/v2/cmd/gosec@latest
 
       - name: Run gosec
-        uses: securego/gosec@master
-        with:
-          # Exclude G101 (hardcoded credentials - false positive on env var names)
-          # Exclude G115 (integer overflow - false positive for PR numbers)
-          # Exclude G304 (file inclusion - intentional for CLI tools)
-          # Exclude G306 (file permissions - config files don't need 0600)
-          args: -exclude=G101,G115,G304,G306 ./...
+        # Individual false positives are suppressed with inline #nosec comments.
+        # Global exclusions for rules that produce widespread false positives:
+        #   G115: integer overflow on safe int<->int64 casts
+        #   G703: path traversal taint (CLI tools intentionally read user-supplied paths)
+        #   G704: SSRF taint (HTTP clients call known GitHub/Slack APIs)
+        #   G705: XSS taint (CLI tools print to stderr, not web responses)
+        #   G706: log injection taint (structured slog logger, not raw string concat)
+        run: gosec -exclude=G115,G703,G704,G705,G706 ./...
 
   build:
     runs-on: ubuntu-latest
@@ -64,17 +66,35 @@ jobs:
 
       - uses: actions/setup-go@v5
         with:
-          go-version: '1.24'
+          go-version: '1.26'
 
       - name: Build
         run: go build -v ./...
 
+  scan:
+    runs-on: ubuntu-latest
+    needs: [build]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Run Trivy vulnerability scanner
+        uses: aquasecurity/trivy-action@master
+        with:
+          scan-type: 'fs'
+          scan-ref: '.'
+          severity: 'CRITICAL,HIGH'
+          exit-code: '1'
+
   deploy:
     runs-on: ubuntu-latest
-    needs: [build, security]
+    needs: [build, security, scan]
     # Only deploy on push to main (not on PRs)
     if: github.event_name == 'push' && github.ref == 'refs/heads/main'
 
+    environment:
+      name: production
+      url: ${{ steps.show-url.outputs.url }}
+
     permissions:
       contents: read
       id-token: write  # Required for Workload Identity Federation
@@ -104,6 +124,7 @@ jobs:
             --project $PROJECT_ID \
             --allow-unauthenticated \
             --env-vars-file=env-cloudrun.yaml \
+            --set-env-vars="GITHUB_APP_ID=${{ secrets.GITHUB_APP_ID }},INSTALLATION_ID=${{ secrets.INSTALLATION_ID }}" \
             --max-instances=10 \
             --cpu=1 \
             --memory=512Mi \
@@ -113,10 +134,11 @@ jobs:
             --platform=managed
 
       - name: Show deployment URL
+        id: show-url
         run: |
           URL=$(gcloud run services describe $SERVICE_NAME \
             --region $REGION \
             --project $PROJECT_ID \
             --format='value(status.url)')
-          echo "🚀 Deployed to: $URL"
-
+          echo "url=$URL" >> $GITHUB_OUTPUT
+          echo "Deployed to: $URL"
diff --git a/.gitignore b/.gitignore
index 37a0615..c92bdff 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,9 @@
 github-copier
 code-copier
 copier
+config-validator
+test-webhook
+test-pem
 *.exe
 *.exe~
 *.dll
diff --git a/.gitleaksignore b/.gitleaksignore
new file mode 100644
index 0000000..4d6ddf7
--- /dev/null
+++ b/.gitleaksignore
@@ -0,0 +1,2 @@
+# Example placeholder string in .env.local.example (not a real key)
+configs/.env.local.example:private-key:77
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d8c909a..fe7f979 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -5,11 +5,16 @@ repos:
     hooks:
       - id: gitleaks
 
-  # Go linting
-  - repo: https://github.com/golangci/golangci-lint
-    rev: v1.62.2
+  # Go linting - requires golangci-lint v2 installed locally:
+  #   go install github.com/golangci/golangci-lint/v2/cmd/golangci-lint@v2.9.0
+  - repo: local
     hooks:
       - id: golangci-lint
+        name: golangci-lint
+        entry: golangci-lint run --fix
+        language: system
+        pass_filenames: false
+        types: [go]
 
   # Local Go hooks
   - repo: local
diff --git a/AGENT.md b/AGENT.md
index ab2277c..06695e9 100644
--- a/AGENT.md
+++ b/AGENT.md
@@ -5,23 +5,42 @@ Webhook service: PR merged → match files → transform paths → copy to targe
 ## File Map
 
 ```
-app.go                              # entrypoint, HTTP server
+app.go                              # entrypoint, HTTP server, graceful shutdown
 services/
-  webhook_handler_new.go            # HandleWebhookWithContainer()
-  workflow_processor.go             # ProcessWorkflow() - core logic
+  webhook_handler_new.go            # HandleWebhookWithContainer() orchestrator
+  workflow_processor.go             # ProcessWorkflow() - core file matching logic
   pattern_matcher.go                # MatchFile(pattern, path) bool
-  github_auth.go                    # ConfigurePermissions() error
-  github_read.go                    # GetFilesChangedInPr(), RetrieveFileContents()
-  github_write_to_target.go         # AddFilesToTargetRepoBranch()
-  github_write_to_source.go         # UpdateDeprecationFile()
-  file_state_service.go             # tracks upload/deprecate queues
+  token_manager.go                  # TokenManager (thread-safe token state, sync.RWMutex)
+  github_auth.go                    # ConfigurePermissions(), JWT generation
+  github_read.go                    # GetFilesChangedInPr() (GraphQL), RetrieveFileContents()
+  github_write_to_target.go         # AddFilesToTargetRepos(), addFilesViaPR()
+  github_write_to_source.go         # UpdateDeprecationFile(filesToDeprecate)
+  rate_limit.go                     # RateLimitTransport (auto-retry on 403/429)
+  delivery_tracker.go               # DeliveryTracker (webhook idempotency via X-GitHub-Delivery)
+  errors.go                         # Sentinel errors (ErrRateLimited, ErrNotFound, etc.)
+  logger.go                         # slog JSON handler, LogCritical, LogAndReturnError
+  file_state_service.go             # Tracks upload/deprecate queues (thread-safe)
   main_config_loader.go             # LoadConfig() with $ref support
+  config_loader.go                  # Config loading & validation
   service_container.go              # DI container
+  health_metrics.go                 # /health (liveness), /ready (readiness), /metrics
+  audit_logger.go                   # MongoDB audit logging
+  slack_notifier.go                 # Slack notifications
+  pr_template_fetcher.go            # PR template resolution from target repos
 types/
   config.go                         # Workflow, Transformation, SourcePattern structs
   types.go                          # ChangedFile, UploadKey, UploadFileContent
 configs/environment.go              # Config struct, LoadEnvironment()
-tests/utils.go                      # test helpers, httpmock setup
+tests/utils.go                      # Test helpers, httpmock setup
+cmd/
+  config-validator/main.go          # CLI: validate configs, test patterns, init templates
+  test-webhook/main.go              # CLI: send test webhook payloads (with delivery ID)
+  test-pem/main.go                  # CLI: verify PEM key + App ID against GitHub API
+scripts/
+  ci-local.sh                       # Run full CI pipeline locally (build, test, lint, vet)
+  run-local.sh                      # Run app locally with dev settings
+  deploy-cloudrun.sh                # Deploy to Google Cloud Run
+  integration-test.sh               # End-to-end integration test
 ```
 
 ## Key Types
@@ -32,11 +51,13 @@ type PatternType string    // "prefix" | "glob" | "regex"
 type TransformationType string  // "move" | "copy" | "glob" | "regex"
 
 type Workflow struct {
-    Name           string
-    Source         SourceConfig      // Repo, Branch, Patterns []SourcePattern
-    Destination    DestinationConfig // Repo, Branch
-    Transformations []Transformation // Type, From, To, Pattern, Replacement
-    Commit         CommitConfig      // Strategy, Message, PRTitle, AutoMerge
+    Name             string
+    Source           Source              // Repo, Branch, InstallationID
+    Destination      Destination         // Repo, Branch
+    Transformations  []Transformation    // Type, From, To, Pattern, Replacement
+    Exclude          []string
+    CommitStrategy   *CommitStrategyConfig // Type (direct|pull_request), PRTitle, PRBody, AutoMerge
+    DeprecationCheck *DeprecationConfig
 }
 
 // types/types.go
@@ -44,15 +65,17 @@ type ChangedFile struct { Path, Status string }  // Status: "ADDED"|"MODIFIED"|"
 type UploadKey struct { RepoName, BranchPath string }
 ```
 
-## Global State (⚠️ mutable)
+## State Management
 
-```go
-// services/github_write_to_target.go
-var FilesToUpload map[UploadKey]UploadFileContent
-// services/github_auth.go
-var InstallationAccessToken string
-var OrgTokens map[string]string
-```
+All mutable state is encapsulated in `TokenManager` (thread-safe via `sync.RWMutex`):
+- Installation access token
+- Per-org installation tokens with expiry
+- Cached JWT
+- HTTP client
+
+Per-request file state is managed via `FileStateService` in the `ServiceContainer`.
+
+Webhook idempotency is handled by `DeliveryTracker` (TTL-based, in-memory).
 
 ## Config Example
 
@@ -62,14 +85,15 @@ workflows:
     source: { repo: "org/src", branch: "main", patterns: [{type: glob, pattern: "docs/**"}] }
     destination: { repo: "org/dest", branch: "main" }
     transformations: [{ type: move, from: "docs/", to: "public/" }]
-    commit: { strategy: pr, message: "Sync" }  # strategy: direct|pr
+    commit_strategy: { type: pull_request, pr_title: "Sync docs" }  # type: direct|pull_request
 ```
 
 ## Test Commands
 
 ```bash
-go test ./...                                    # all
+go test -race ./...                              # all with race detector
 go test ./services/... -run TestWorkflow -v      # specific
+golangci-lint run ./...                          # lint
 ```
 
 ## Edit Patterns
@@ -80,11 +104,17 @@ go test ./services/... -run TestWorkflow -v      # specific
 | New pattern type | `types/config.go` (PatternType) → `pattern_matcher.go` |
 | New config field | `types/config.go` (struct) → consumers in `workflow_processor.go` |
 | Webhook logic | `webhook_handler_new.go` |
+| Rate limit behavior | `rate_limit.go` |
+| Auth flow | `github_auth.go` + `token_manager.go` |
+| CLI tool | `cmd/<tool>/main.go` + `cmd/<tool>/README.md` |
 
 ## Conventions
 
 - Return `error`, never `log.Fatal`
 - Wrap errors: `fmt.Errorf("context: %w", err)`
+- Use sentinel errors from `errors.go` where appropriate
 - Nil-check GitHub API responses before dereference
+- Use `log/slog` for all logging (never `log` or `fmt.Print` for operational output)
 - Tests use `httpmock`; see `tests/utils.go`
+- Always run tests with `-race` flag
 - **Changelog**: Update `CHANGELOG.md` for all notable changes (follows [Keep a Changelog](https://keepachangelog.com/en/1.1.0/))
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 96daa5d..8a2e9c8 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -2,6 +2,32 @@
 
 All notable changes to this project will be documented in this file.
 
+## Feb 2026
+
+### Added
+- **Rate limit handling** - Custom `RateLimitTransport` (`services/rate_limit.go`) automatically detects 403/429 responses with `X-RateLimit-Remaining` / `Retry-After` headers and retries with backoff
+- **Webhook idempotency** - `DeliveryTracker` (`services/delivery_tracker.go`) deduplicates webhook deliveries using `X-GitHub-Delivery` header with TTL-based cleanup
+- **Structured logging** - Migrated from `log` to `log/slog` with JSON handler (`services/logger.go`); compatible with Google Cloud Logging severity levels including custom `CRITICAL`
+- **Sentinel errors** - Centralized error definitions in `services/errors.go` (`ErrRateLimited`, `ErrNotFound`, etc.)
+- **Token manager** - Thread-safe `TokenManager` (`services/token_manager.go`) with `sync.RWMutex` for concurrent token access
+- **Readiness endpoint** - `/ready` probe checks GitHub auth, rate limit headroom, and MongoDB connectivity
+- **GitHub App manifest** - `github-app-manifest.yml` documenting required permissions and events
+- **Integration tests** - End-to-end tests for webhook processing pipeline (`services/integration_test.go`), GitHub auth flow, and extracted helper functions
+- **CI/CD improvements** - Added gosec security scanning, Trivy vulnerability scanning, GitHub Environment deployment gates
+
+### Changed
+- **Go version** - Upgraded from 1.24.0 to 1.26.0
+- **go-github** - Upgraded from v48 to v82 (`github.String` → `github.Ptr`, updated API signatures)
+- **mongo-driver** - Upgraded from v1 to v2 (updated import paths, API changes)
+- **Error handling** - All errors wrapped with `%w` for `errors.Is()`/`errors.As()` compatibility; removed bare `log.Fatal` calls
+- **Function decomposition** - Broke up `handleMergedPRWithContainer` (→ 5 helpers) and `addFilesViaPR` (→ 3 helpers) for readability
+- **Dot imports** - Removed all dot imports for explicit package references
+- **Health endpoint** - Split into `/health` (liveness) and `/ready` (readiness) with deep dependency checks
+- **HTTP method check** - Webhook handler rejects non-POST requests with 405
+- **MongoDB timeouts** - Configured explicit connection, server selection, and operation timeouts
+- **Dockerfile** - Pinned base image, added non-root user, added `HEALTHCHECK` instruction
+- **Environment config** - Moved org-specific values to deployment-time configuration; committed env file contains only non-secret defaults
+
 ## 17 Dec 2025
 
 ### Added
diff --git a/Dockerfile b/Dockerfile
index 2bedd4f..bbbb6af 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,5 @@
 # Build stage
-FROM golang:1.24.0-alpine AS builder
+FROM golang:1.26.0-alpine AS builder
 
 # Install build dependencies
 RUN apk add --no-cache git ca-certificates
@@ -16,23 +16,32 @@ COPY . .
 # Build the binary
 # CGO_ENABLED=0 for static binary (no C dependencies)
 # -ldflags="-w -s" strips debug info to reduce size
-RUN CGO_ENABLED=0 GOOS=linux go build -ldflags="-w -s" -o examples-copier .
+RUN CGO_ENABLED=0 GOOS=linux go build -ldflags="-w -s" -o github-copier .
 
-# Runtime stage
-FROM alpine:latest
+# Runtime stage - pin to specific version for reproducible builds
+FROM alpine:3.21
 
 # Install ca-certificates for HTTPS requests
 RUN apk --no-cache add ca-certificates
 
-WORKDIR /root/
+# Create non-root user
+RUN addgroup -S appgroup && adduser -S appuser -G appgroup
+
+WORKDIR /home/appuser
 
 # Copy binary from builder
-COPY --from=builder /app/examples-copier .
+COPY --from=builder /app/github-copier .
+
+# Switch to non-root user
+USER appuser
 
 # Cloud Run sets PORT environment variable
 # Our app reads it from config.Port (defaults to 8080)
 EXPOSE 8080
 
+HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \
+    CMD wget --no-verbose --tries=1 --spider http://localhost:8080/health || exit 1
+
 # Run the binary
-CMD ["./examples-copier"]
+CMD ["./github-copier"]
 
diff --git a/Makefile b/Makefile
index b586e4c..080998c 100644
--- a/Makefile
+++ b/Makefile
@@ -2,7 +2,7 @@
 
 # Default target
 help:
-	@echo "Examples Copier - Makefile"
+	@echo "GitHub Copier - Makefile"
 	@echo ""
 	@echo "Available targets:"
 	@echo "  make build              - Build all binaries"
@@ -27,8 +27,8 @@ help:
 
 # Build all binaries
 build:
-	@echo "Building examples-copier..."
-	@go build -o examples-copier .
+	@echo "Building github-copier..."
+	@go build -o github-copier .
 	@echo "Building config-validator..."
 	@go build -o config-validator ./cmd/config-validator
 	@echo "Building test-webhook..."
@@ -42,7 +42,7 @@ test: test-unit
 # Run unit tests
 test-unit:
 	@echo "Running unit tests..."
-	@go test ./services -v
+	@go test -race ./services -v
 
 # Run unit tests with coverage
 test-coverage:
@@ -100,28 +100,28 @@ test-pr:
 
 # Run application
 run: build
-	@echo "Starting examples-copier..."
-	@./examples-copier
+	@echo "Starting github-copier..."
+	@./github-copier
 
 # Run in dry-run mode
 run-dry: build
-	@echo "Starting examples-copier in dry-run mode..."
-	@DRY_RUN=true ./examples-copier
+	@echo "Starting github-copier in dry-run mode..."
+	@DRY_RUN=true ./github-copier
 
 # Run in local development mode (recommended)
 run-local: build
-	@echo "Starting examples-copier in local development mode..."
+	@echo "Starting github-copier in local development mode..."
 	@./scripts/run-local.sh
 
 # Run with cloud logging disabled (quick local testing)
 run-local-quick: build
-	@echo "Starting examples-copier (local, no cloud logging)..."
-	@COPIER_DISABLE_CLOUD_LOGGING=true DRY_RUN=true ./examples-copier
+	@echo "Starting github-copier (local, no cloud logging)..."
+	@COPIER_DISABLE_CLOUD_LOGGING=true DRY_RUN=true ./github-copier
 
 # Validate configuration
 validate: build
 	@echo "Validating configuration..."
-	@./examples-copier -validate
+	@./github-copier -validate
 
 # Install binaries to $GOPATH/bin
 install:
@@ -129,12 +129,13 @@ install:
 	@go install .
 	@go install ./cmd/config-validator
 	@go install ./cmd/test-webhook
+	@go install ./cmd/test-pem
 	@echo "✓ Binaries installed to \$$GOPATH/bin"
 
 # Clean built binaries
 clean:
 	@echo "Cleaning built binaries..."
-	@rm -f examples-copier config-validator test-webhook
+	@rm -f github-copier config-validator test-webhook test-pem
 	@rm -f coverage.out coverage.html
 	@echo "✓ Clean complete"
 
diff --git a/QUICK-REFERENCE.md b/QUICK-REFERENCE.md
deleted file mode 100644
index 28fe49a..0000000
--- a/QUICK-REFERENCE.md
+++ /dev/null
@@ -1,544 +0,0 @@
-# Quick Reference Guide
-
-## Command Line
-
-### Application
-
-```bash
-# Run with default settings
-./github-copier
-
-# Run with custom environment
-./github-copier -env ./configs/.env.production
-
-# Dry-run mode (no actual commits)
-./github-copier -dry-run
-
-# Validate configuration only
-./github-copier -validate
-
-# Show help
-./github-copier -help
-```
-
-### CLI Validator
-
-```bash
-# Validate config
-./config-validator validate -config copier-config.yaml -v
-
-# Test pattern
-./config-validator test-pattern -type regex -pattern "^examples/(?P<lang>[^/]+)/.*$" -file "examples/go/main.go"
-
-# Test transformation
-./config-validator test-transform -source "examples/go/main.go" -template "docs/${lang}/${file}" -vars "lang=go,file=main.go"
-
-# Initialize new config
-./config-validator init -output copier-config.yaml
-
-# Convert formats
-./config-validator convert -input config.json -output copier-config.yaml
-```
-
-## Configuration Patterns
-
-### Move Transformation
-```yaml
-transformations:
-  - move:
-      from: "examples/go"
-      to: "code/go"
-```
-
-### Glob Transformation
-```yaml
-transformations:
-  - glob:
-      pattern: "examples/*/main.go"
-      transform: "code/${relative_path}"
-```
-
-### Regex Transformation
-```yaml
-transformations:
-  - regex:
-      pattern: "^examples/(?P<lang>[^/]+)/(?P<file>.+)$"
-      transform: "code/${lang}/${file}"
-```
-
-### Workflow with Exclusions
-```yaml
-workflows:
-  - name: "Copy examples"
-    transformations:
-      - move:
-          from: "examples"
-          to: "code"
-    exclude:
-      - "**/.gitignore"
-      - "**/node_modules/**"
-      - "**/.env"
-      - "**/dist/**"
-```
-
-## Path Transformations
-
-Path transformations are used with **`glob`** and **`regex`** transformation types using the `transform` parameter.
-
-### Built-in Variables
-- `${path}` - Full source path
-- `${filename}` - File name only
-- `${dir}` - Directory path
-- `${ext}` - File extension
-- `${relative_path}` - Path relative to glob pattern prefix (glob only)
-
-### Glob Transformation Examples
-```yaml
-# Keep same path
-transformations:
-  - glob:
-      pattern: "examples/**/*.go"
-      transform: "${path}"
-
-# Change directory
-transformations:
-  - glob:
-      pattern: "examples/**/*.go"
-      transform: "docs/${relative_path}"
-
-# Reorganize structure (using custom variables from regex)
-transformations:
-  - regex:
-      pattern: "^examples/(?P<lang>[^/]+)/(?P<category>[^/]+)/(?P<file>.+)$"
-      transform: "docs/${lang}/${category}/${file}"
-
-# Change extension
-transformations:
-  - glob:
-      pattern: "examples/**/*.txt"
-      transform: "${dir}/${filename}.md"
-```
-
-## Commit Strategies
-
-### Direct Commit
-```yaml
-commit_strategy:
-  type: "direct"
-  commit_message: "Update examples"
-```
-
-### Pull Request
-```yaml
-commit_strategy:
-  type: "pull_request"
-  commit_message: "Update examples"
-  pr_title: "Update code examples"
-  pr_body: "Automated update"
-  use_pr_template: true  # Fetch PR template from target repo
-  auto_merge: true
-```
-
-## Advanced Features
-
-### Exclude Patterns
-Exclude unwanted files from being copied at the workflow level:
-
-```yaml
-workflows:
-  - name: "Copy examples"
-    exclude:
-      - "**/.gitignore"      # Exclude .gitignore
-      - "**/node_modules/**" # Exclude dependencies
-      - "**/.env"            # Exclude .env files
-      - "**/.env.*"          # Exclude .env.local, .env.production, etc.
-      - "**/dist/**"         # Exclude build output
-      - "**/build/**"        # Exclude build artifacts
-      - "**/*.test.js"       # Exclude test files
-```
-
-### PR Template Integration
-Fetch and merge PR templates from target repos:
-
-```yaml
-commit_strategy:
-  type: "pull_request"
-  pr_body: |
-    🤖 Automated update
-    Files: ${file_count}
-  use_pr_template: true  # Fetches .github/pull_request_template.md
-```
-
-**Result:** PR description shows:
-1. Target repo's PR template (checklists, guidelines)
-2. Separator (`---`)
-3. Your configured content (automation info)
-
-## Message Templates
-
-### Available Variables
-- `${rule_name}` - Copy rule name (e.g., "java-aggregation-examples")
-- `${source_repo}` - Source repository (e.g., "mongodb/aggregation-tasks")
-- `${target_repo}` - Target repository (e.g., "mongodb/vector-search")
-- `${source_branch}` - Source branch (e.g., "main")
-- `${target_branch}` - Target branch (e.g., "main")
-- `${file_count}` - Number of files (e.g., "3")
-- `${pr_number}` - Source PR number (e.g., "42")
-- `${commit_sha}` - Source commit SHA (e.g., "abc123")
-- Custom variables from regex patterns (e.g., `${lang}`, `${file}`)
-
-### Examples
-```yaml
-commit_message: "Update ${category} examples from ${lang}"
-pr_title: "Update ${lang} examples"
-pr_body: |
-  Files updated: ${file_count} using ${rule_name} match pattern
-
-  Source: ${source_repo}
-  PR: #${pr_number}
-```
-
-## API Endpoints
-
-### Health Check
-```bash
-curl http://localhost:8080/health
-```
-
-### Metrics
-```bash
-curl http://localhost:8080/metrics
-```
-
-### Webhook
-```bash
-curl -X POST http://localhost:8080/webhook \
-  -H "Content-Type: application/json" \
-  -H "X-Hub-Signature-256: sha256=..." \
-  -d @webhook-payload.json
-```
-
-## Environment Variables
-
-### Required
-```bash
-REPO_OWNER=your-org
-REPO_NAME=your-repo
-GITHUB_APP_ID=123456
-GITHUB_INSTALLATION_ID=789012
-GCP_PROJECT_ID=your-project
-PEM_KEY_NAME=projects/123/secrets/KEY/versions/latest
-```
-
-### Optional
-```bash
-# Application
-PORT=8080
-CONFIG_FILE=copier-config.yaml
-DEPRECATION_FILE=deprecated_examples.json
-DRY_RUN=false
-
-# Logging
-LOG_LEVEL=info
-COPIER_DEBUG=false
-COPIER_DISABLE_CLOUD_LOGGING=false
-
-# Audit
-AUDIT_ENABLED=true
-MONGO_URI=mongodb+srv://...
-AUDIT_DATABASE=code_copier
-AUDIT_COLLECTION=audit_events
-
-# Metrics
-METRICS_ENABLED=true
-
-# Webhook
-WEBHOOK_SECRET=your-secret
-```
-
-## MongoDB Queries
-
-### Recent Events
-```javascript
-db.audit_events.find().sort({timestamp: -1}).limit(10)
-```
-
-### Failed Operations
-```javascript
-db.audit_events.find({success: false}).sort({timestamp: -1})
-```
-
-### Events by Rule
-```javascript
-db.audit_events.find({rule_name: "Copy Go examples"})
-```
-
-### Statistics
-```javascript
-db.audit_events.aggregate([
-  {$match: {event_type: "copy"}},
-  {$group: {
-    _id: "$rule_name",
-    count: {$sum: 1},
-    avg_duration: {$avg: "$duration_ms"}
-  }}
-])
-```
-
-### Success Rate
-```javascript
-db.audit_events.aggregate([
-  {$group: {
-    _id: "$success",
-    count: {$sum: 1}
-  }}
-])
-```
-
-## Testing
-
-### Run Unit Tests
-```bash
-# All tests
-go test ./services -v
-
-# Specific test
-go test ./services -v -run TestPatternMatcher
-
-# With coverage
-go test ./services -cover
-```
-
-### Test with Webhooks
-
-#### Option 1: Use Example Payload
-```bash
-# Build test tool
-go build -o test-webhook ./cmd/test-webhook
-
-# Send example payload
-./test-webhook -payload testdata/example-pr-merged.json
-
-# Dry-run (see payload without sending)
-./test-webhook -payload testdata/example-pr-merged.json -dry-run
-```
-
-#### Option 2: Use Real PR Data
-```bash
-# Set GitHub token
-export GITHUB_TOKEN=ghp_your_token_here
-
-# Fetch and send real PR data
-./test-webhook -pr 123 -owner myorg -repo myrepo
-
-# Test against production
-./test-webhook -pr 123 -owner myorg -repo myrepo \
-  -url https://myapp.appspot.com/webhook \
-  -secret "my-webhook-secret"
-```
-
-#### Option 3: Use Helper Script (Interactive)
-```bash
-# Make executable
-chmod +x scripts/test-with-pr.sh
-
-# Run interactive test
-./scripts/test-with-pr.sh 123 myorg myrepo
-```
-
-### Test in Dry-Run Mode
-```bash
-# Start app in dry-run mode
-DRY_RUN=true ./github-copier &
-
-# Send test webhook
-./test-webhook -pr 123 -owner myorg -repo myrepo
-
-# Check logs (no actual commits made)
-```
-
-### Build
-```bash
-# Main application
-go build -o github-copier .
-
-# CLI validator
-go build -o config-validator ./cmd/config-validator
-
-# Test webhook tool
-go build -o test-webhook ./cmd/test-webhook
-
-# All tools
-go build -o github-copier . && \
-go build -o config-validator ./cmd/config-validator && \
-go build -o test-webhook ./cmd/test-webhook
-```
-
-## Common Patterns
-
-### Copy All Go Files
-```yaml
-workflows:
-  - name: "Copy Go files"
-    source:
-      repo: "org/source"
-      branch: "main"
-    destination:
-      repo: "org/docs"
-      branch: "main"
-    transformations:
-      - regex:
-          pattern: "^examples/.*\\.go$"
-          transform: "code/${path}"
-```
-
-### Organize by Language
-```yaml
-workflows:
-  - name: "Organize by language"
-    transformations:
-      - regex:
-          pattern: "^examples/(?P<lang>[^/]+)/(?P<rest>.+)$"
-          transform: "languages/${lang}/${rest}"
-```
-
-### Multiple Workflows for Different Destinations
-```yaml
-workflows:
-  - name: "Copy to docs-v1"
-    destination:
-      repo: "org/docs-v1"
-      branch: "main"
-    transformations:
-      - move:
-          from: "examples"
-          to: "examples"
-
-  - name: "Copy to docs-v2"
-    destination:
-      repo: "org/docs-v2"
-      branch: "main"
-    transformations:
-      - move:
-          from: "examples"
-          to: "code-samples"
-```
-
-### Conditional Copying (by file type)
-```yaml
-workflows:
-  - name: "Copy by file type"
-    transformations:
-      - regex:
-          pattern: "^examples/.*\\.(?P<ext>go|py|js)$"
-          transform: "code/${ext}/${filename}"
-```
-
-## Troubleshooting
-
-### Check Logs
-```bash
-# Application logs
-gcloud app logs tail -s default
-
-# Local logs
-LOG_LEVEL=debug ./github-copier
-```
-
-### Validate Config
-```bash
-./config-validator validate -config copier-config.yaml -v
-```
-
-### Test Pattern Matching
-```bash
-./config-validator test-pattern \
-  -type regex \
-  -pattern "your-pattern" \
-  -file "test/file.go"
-```
-
-### Dry Run
-```bash
-DRY_RUN=true ./github-copier
-```
-
-### Check Health
-```bash
-curl http://localhost:8080/health
-```
-
-### Check Metrics
-```bash
-curl http://localhost:8080/metrics | jq
-```
-
-## Deployment 
-
-### Google Cloud Quick Commands
-
-```bash
-# Deploy (env.yaml is included via 'includes' directive in app.yaml)
-gcloud app deploy app.yaml
-
-# View logs
-gcloud app logs tail -s default
-
-# Check health
-curl https://github-copy-code-examples.appspot.com/health
-
-# List secrets
-gcloud secrets list
-
-# Grant access
-./grant-secret-access.sh
-```
-
-
-
-## File Locations
-
-```
-github-copier/
-├── README.md                 # Main documentation
-├── QUICK-REFERENCE.md        # This file
-├── docs/
-│   ├── ARCHITECTURE.md       # Architecture overview
-│   ├── CONFIGURATION-GUIDE.md # Complete config reference
-│   ├── DEPLOYMENT.md         # Deployment guide
-│   ├── DEPLOYMENT-CHECKLIST.md  # Deployment checklist
-│   ├── FAQ.md                # Frequently asked questions
-│   ├── LOCAL-TESTING.md      # Local testing guide
-│   ├── PATTERN-MATCHING-GUIDE.md # Pattern matching guide
-│   ├── PATTERN-MATCHING-CHEATSHEET.md # Quick pattern reference
-│   ├── TROUBLESHOOTING.md    # Troubleshooting guide
-│   └── WEBHOOK-TESTING.md    # Webhook testing guide
-├── configs/
-│   ├── .env                  # Environment config
-│   ├── env.yaml.example      # Environment template
-│   └── copier-config.example.yaml # Config template
-└── cmd/
-    ├── config-validator/     # CLI validation tool
-    └── test-webhook/         # Webhook testing tool
-```
-
-## Quick Start Checklist
-
-- [ ] Clone repository
-- [ ] Copy `configs/.env.local.example` to `configs/.env`
-- [ ] Set required environment variables
-- [ ] Create `copier-config.yaml` in source repo
-- [ ] Validate config: `./config-validator validate -config copier-config.yaml`
-- [ ] Test in dry-run: `DRY_RUN=true ./github-copier`
-- [ ] Deploy: `./github-copier`
-- [ ] Configure GitHub webhook
-- [ ] Monitor: `curl http://localhost:8080/health`
-
-## Support
-
-- **Documentation**: [README.md](README.md)
-- **Configuration**: [Configuration Guide](./docs/CONFIGURATION-GUIDE.md)
-- **Deployment**: [Deployment Guide](./docs/DEPLOYMENT.md)
-- **Troubleshooting**: [Troubleshooting Guide](./docs/TROUBLESHOOTING.md)
-- **FAQ**: [Frequently Asked Questions](./docs/FAQ.md)
-
diff --git a/README.md b/README.md
index db0a9aa..264b5a5 100644
--- a/README.md
+++ b/README.md
@@ -22,7 +22,10 @@ A GitHub app that automatically copies code examples and files from source repos
 - **PR Template Integration** - Fetch and merge PR templates from target repos
 - **File Exclusion** - Exclude patterns to filter out unwanted files
 - **Audit Logging** - MongoDB-based event tracking for all operations
-- **Health & Metrics** - `/health` and `/metrics` endpoints for monitoring
+- **Health & Metrics** - `/health`, `/ready`, and `/metrics` endpoints for monitoring
+- **Rate Limit Handling** - Automatic GitHub API rate limit detection, backoff, and retry
+- **Webhook Idempotency** - Deduplication via `X-GitHub-Delivery` header tracking
+- **Structured Logging** - JSON structured logging via `log/slog` (Cloud Logging compatible)
 - **Development Tools** - Dry-run mode, CLI validation, enhanced logging
 - **Thread-Safe** - Concurrent webhook processing with proper state management
 
@@ -30,7 +33,7 @@ A GitHub app that automatically copies code examples and files from source repos
 
 ### Prerequisites
 
-- Go 1.23.4+
+- Go 1.26+
 - GitHub App credentials
 - Google Cloud project (for Secret Manager and logging)
 - MongoDB Atlas (optional, for audit logging)
@@ -358,29 +361,20 @@ Validate and test configurations before deployment:
 
 ## Monitoring
 
-### Health Endpoint
+### Health Endpoint (Liveness)
 
-Check application health:
+Basic liveness check:
 
 ```bash
 curl http://localhost:8080/health
 ```
 
-Response:
-```json
-{
-  "status": "healthy",
-  "started": true,
-  "github": {
-    "status": "healthy",
-    "authenticated": true
-  },
-  "queues": {
-    "upload_count": 0,
-    "deprecation_count": 0
-  },
-  "uptime": "1h23m45s"
-}
+### Readiness Endpoint
+
+Deep readiness probe (checks GitHub auth, rate limits, MongoDB):
+
+```bash
+curl http://localhost:8080/ready
 ```
 
 ### Metrics Endpoint
@@ -391,31 +385,6 @@ Get performance metrics:
 curl http://localhost:8080/metrics
 ```
 
-Response:
-```json
-{
-  "webhooks": {
-    "received": 42,
-    "processed": 40,
-    "failed": 2,
-    "success_rate": 95.24,
-    "processing_time": {
-      "avg_ms": 234.5,
-      "p50_ms": 200,
-      "p95_ms": 450,
-      "p99_ms": 890
-    }
-  },
-  "files": {
-    "matched": 150,
-    "uploaded": 145,
-    "upload_failed": 5,
-    "deprecated": 3,
-    "upload_success_rate": 96.67
-  }
-}
-```
-
 ## Audit Logging
 
 When enabled, all operations are logged to MongoDB:
@@ -445,18 +414,18 @@ db.audit_events.aggregate([
 
 ## Testing
 
-### Run Unit Tests
+### Run Tests
 
 ```bash
-# Run all tests
-go test ./services -v
+# Run all tests with race detector
+go test -race ./...
 
 # Run specific test suite
 go test ./services -v -run TestPatternMatcher
 
 # Run with coverage
-go test ./services -cover
-go test ./services -coverprofile=coverage.out
+go test -race ./services -cover
+go test -race ./services -coverprofile=coverage.out
 go tool cover -html=coverage.out
 ```
 
@@ -476,9 +445,9 @@ In dry-run mode:
 - Audit events are logged
 - **NO actual commits or PRs are created**
 
-### Enhanced Logging
+### Structured Logging
 
-Enable detailed logging:
+The app uses `log/slog` with JSON output. Enable debug logging:
 
 ```bash
 LOG_LEVEL=debug ./github-copier
@@ -493,6 +462,7 @@ COPIER_DEBUG=true ./github-copier
 ```
 github-copier/
 ├── app.go                    # Main application entry point
+├── github-app-manifest.yml   # GitHub App permissions documentation
 ├── cmd/
 │   ├── config-validator/     # CLI validation tool
 │   └── test-webhook/         # Webhook testing tool
@@ -502,26 +472,34 @@ github-copier/
 │   ├── env.yaml.example      # YAML environment template
 │   └── copier-config.example.yaml # Config template
 ├── services/
-│   ├── pattern_matcher.go    # Pattern matching engine
-│   ├── config_loader.go      # Config loading & validation
-│   ├── audit_logger.go       # MongoDB audit logging
-│   ├── health_metrics.go     # Health & metrics endpoints
-│   ├── file_state_service.go # Thread-safe state management
-│   ├── service_container.go  # Dependency injection
-│   ├── webhook_handler_new.go # Webhook handler
-│   ├── github_auth.go        # GitHub authentication
-│   ├── github_read.go        # GitHub read operations
+│   ├── webhook_handler_new.go # Webhook handler (orchestrator)
+│   ├── workflow_processor.go  # ProcessWorkflow() - core logic
+│   ├── pattern_matcher.go     # Pattern matching engine
+│   ├── config_loader.go       # Config loading & validation
+│   ├── main_config_loader.go  # Main config with $ref support
+│   ├── github_auth.go         # GitHub App authentication
+│   ├── github_read.go         # GitHub read operations (REST + GraphQL)
 │   ├── github_write_to_target.go # GitHub write operations
-│   └── slack_notifier.go     # Slack notifications
+│   ├── github_write_to_source.go # Deprecation file updates
+│   ├── token_manager.go       # Thread-safe token state management
+│   ├── rate_limit.go          # GitHub API rate limit handling
+│   ├── delivery_tracker.go    # Webhook idempotency (deduplication)
+│   ├── errors.go              # Sentinel errors
+│   ├── logger.go              # Structured logging (slog)
+│   ├── service_container.go   # Dependency injection container
+│   ├── file_state_service.go  # Thread-safe upload/deprecation queues
+│   ├── health_metrics.go      # Health, readiness & metrics endpoints
+│   ├── audit_logger.go        # MongoDB audit logging
+│   ├── slack_notifier.go      # Slack notifications
+│   └── pr_template_fetcher.go # PR template resolution
 ├── types/
-│   ├── config.go             # Configuration types
-│   └── types.go              # Core types
+│   ├── config.go              # Configuration types
+│   └── types.go               # Core types
 └── docs/
-    ├── ARCHITECTURE.md       # Architecture overview
-    ├── CONFIGURATION-GUIDE.md # Complete config reference
-    ├── DEPLOYMENT.md         # Deployment guide
-    ├── FAQ.md                # Frequently asked questions
-    └── ...                   # Additional documentation
+    ├── ARCHITECTURE.md        # Architecture overview
+    ├── DEPLOYMENT.md          # Deployment guide (Cloud Run)
+    ├── FAQ.md                 # Frequently asked questions
+    └── ...                    # Additional documentation
 ```
 
 ### Service Container
@@ -554,19 +532,20 @@ docker run -p 8080:8080 --env-file env.yaml github-copier
 ## Security
 
 - **Webhook Signature Verification** - HMAC-SHA256 validation
+- **Webhook Idempotency** - Duplicate delivery detection via `X-GitHub-Delivery`
 - **Secret Management** - Google Cloud Secret Manager
-- **Least Privilege** - Minimal GitHub App permissions
+- **Least Privilege** - Minimal GitHub App permissions (see `github-app-manifest.yml`)
 - **Audit Trail** - Complete operation logging
 
 ## Documentation
 
 ### Getting Started
 
-- **[Main Config README](configs/copier-config-examples/MAIN-CONFIG-README.md)** - Complete main config documentation
-- **[Quick Start Guide](configs/copier-config-examples/QUICK-START-MAIN-CONFIG.md)** - Get started in 5 minutes
+- **[Main Config README](configs/copier-config-examples/MAIN-CONFIG-README.md)** - Main config architecture
+- **[Source Repo README](configs/copier-config-examples/SOURCE-REPO-README.md)** - Workflow config guide for source repos
 - **[Pattern Matching Guide](docs/PATTERN-MATCHING-GUIDE.md)** - Pattern matching with examples
 - **[Local Testing](docs/LOCAL-TESTING.md)** - Test locally before deploying
-- **[Deployment Guide](docs/DEPLOYMENT.md)** - Deploy to production
+- **[Deployment Guide](docs/DEPLOYMENT.md)** - Deploy to Cloud Run
 
 ### Reference
 
@@ -579,7 +558,10 @@ docker run -p 8080:8080 --env-file env.yaml github-copier
 
 - **[Slack Notifications](docs/SLACK-NOTIFICATIONS.md)** - Slack integration guide
 - **[Webhook Testing](docs/WEBHOOK-TESTING.md)** - Test with real PR data
+- **[GitHub App Manifest](github-app-manifest.yml)** - Required permissions and events
 
 ### Tools
 
+- **[Config Validator](cmd/config-validator/README.md)** - CLI tool for validating configs
+- **[Test Webhook](cmd/test-webhook/README.md)** - CLI tool for testing webhooks
 - **[Scripts](scripts/README.md)** - Helper scripts for deployment and testing
diff --git a/app.go b/app.go
index f104059..3a7de17 100644
--- a/app.go
+++ b/app.go
@@ -4,7 +4,6 @@ import (
 	"context"
 	"flag"
 	"fmt"
-	"log"
 	"net/http"
 	"os"
 	"os/signal"
@@ -40,12 +39,13 @@ func main() {
 	}
 
 	// Load secrets from Secret Manager if not directly provided
-	if err := services.LoadWebhookSecret(config); err != nil {
+	ctx := context.Background()
+	if err := services.LoadWebhookSecret(ctx, config); err != nil {
 		fmt.Printf("❌ Error loading webhook secret: %v\n", err)
 		os.Exit(1)
 	}
 
-	if err := services.LoadMongoURI(config); err != nil {
+	if err := services.LoadMongoURI(ctx, config); err != nil {
 		fmt.Printf("❌ Error loading MongoDB URI: %v\n", err)
 		os.Exit(1)
 	}
@@ -61,7 +61,7 @@ func main() {
 		fmt.Printf("❌ Failed to initialize services: %v\n", err)
 		os.Exit(1)
 	}
-	defer container.Close(context.Background())
+	defer func() { _ = container.Close(context.Background()) }()
 
 	// If validate-only mode, validate config and exit
 	if validateOnly {
@@ -74,11 +74,11 @@ func main() {
 	}
 
 	// Initialize Google Cloud logging
-	services.InitializeGoogleLogger()
+	services.InitializeLogger(config)
 	defer services.CloseGoogleLogger()
 
 	// Configure GitHub permissions
-	if err := services.ConfigurePermissions(); err != nil {
+	if err := services.ConfigurePermissions(ctx, config); err != nil {
 		fmt.Printf("❌ Failed to configure GitHub permissions: %v\n", err)
 		os.Exit(1)
 	}
@@ -140,8 +140,11 @@ func startWebServer(config *configs.Config, container *services.ServiceContainer
 		handleWebhook(w, r, config, container)
 	})
 
-	// Health endpoint
-	mux.HandleFunc("/health", services.HealthHandler(container.FileStateService, container.StartTime))
+	// Liveness probe — lightweight, always 200 if process is running
+	mux.HandleFunc("/health", services.HealthHandler(container.StartTime))
+
+	// Readiness probe — checks GitHub auth, MongoDB connectivity
+	mux.HandleFunc("/ready", services.ReadinessHandler(container))
 
 	// Metrics endpoint (if enabled)
 	if config.MetricsEnabled {
@@ -155,11 +158,12 @@ func startWebServer(config *configs.Config, container *services.ServiceContainer
 			return
 		}
 		w.Header().Set("Content-Type", "text/plain")
-		fmt.Fprintf(w, "GitHub Code Example Copier\n")
-		fmt.Fprintf(w, "Webhook endpoint: %s\n", config.WebserverPath)
-		fmt.Fprintf(w, "Health check: /health\n")
+		_, _ = fmt.Fprintf(w, "GitHub Code Example Copier\n")
+		_, _ = fmt.Fprintf(w, "Webhook endpoint: %s\n", config.WebserverPath)
+		_, _ = fmt.Fprintf(w, "Health check: /health\n")
+		_, _ = fmt.Fprintf(w, "Readiness check: /ready\n")
 		if config.MetricsEnabled {
-			fmt.Fprintf(w, "Metrics: /metrics\n")
+			_, _ = fmt.Fprintf(w, "Metrics: /metrics\n")
 		}
 	})
 
@@ -178,7 +182,7 @@ func startWebServer(config *configs.Config, container *services.ServiceContainer
 
 	// Start server in goroutine
 	go func() {
-		services.LogInfo(fmt.Sprintf("Starting web server on port %s", port))
+		services.LogInfo("Starting web server", "port", port)
 		if err := server.ListenAndServe(); err != nil && err != http.ErrServerClosed {
 			serverErr <- fmt.Errorf("server error: %w", err)
 		}
@@ -196,27 +200,27 @@ func startWebServer(config *configs.Config, container *services.ServiceContainer
 			return err
 		}
 	case sig := <-sigChan:
-		log.Printf("Received signal %v, initiating graceful shutdown...", sig)
+		services.LogInfo("Received signal, initiating graceful shutdown", "signal", sig)
 	}
 
 	// Graceful shutdown with timeout
 	shutdownCtx, cancel := context.WithTimeout(context.Background(), 30*time.Second)
 	defer cancel()
 
-	log.Println("Waiting for in-flight requests to complete...")
+	services.LogInfo("Waiting for in-flight requests to complete")
 	if err := server.Shutdown(shutdownCtx); err != nil {
-		log.Printf("Server shutdown error: %v", err)
+		services.LogError("Server shutdown error", "error", err)
 	} else {
-		log.Println("Server stopped accepting new connections")
+		services.LogInfo("Server stopped accepting new connections")
 	}
 
 	// Cleanup resources (flush audit logs, close connections)
-	log.Println("Cleaning up resources...")
+	services.LogInfo("Cleaning up resources")
 	if err := container.Close(shutdownCtx); err != nil {
-		log.Printf("Cleanup error: %v", err)
+		services.LogError("Cleanup error", "error", err)
 	}
 
-	log.Println("Shutdown complete")
+	services.LogInfo("Shutdown complete")
 	return nil
 }
 
diff --git a/app.yaml b/app.yaml
deleted file mode 100644
index 6c78988..0000000
--- a/app.yaml
+++ /dev/null
@@ -1,44 +0,0 @@
-runtime: go
-runtime_config:
-  operating_system: "ubuntu22"
-  runtime_version: "1.23"
-env: flex
-
-includes:
-  - env.yaml
-
-# Automatic scaling configuration
-# Keeps at least 1 instance running to avoid cold starts
-automatic_scaling:
-  min_num_instances: 1
-  max_num_instances: 10
-  cool_down_period_sec: 120
-  cpu_utilization:
-    target_utilization: 0.6
-
-# Network configuration
-network:
-  session_affinity: true
-
-# Health check configuration
-# These ensure the app is ready before receiving traffic
-liveness_check:
-  path: "/health"
-  check_interval_sec: 30
-  timeout_sec: 4
-  failure_threshold: 2
-  success_threshold: 2
-
-readiness_check:
-  path: "/health"
-  check_interval_sec: 5
-  timeout_sec: 4
-  failure_threshold: 2
-  success_threshold: 2
-  app_start_timeout_sec: 300
-
-# Resources configuration
-resources:
-  cpu: 1
-  memory_gb: 2
-  disk_size_gb: 10
diff --git a/cmd/config-validator/README.md b/cmd/config-validator/README.md
index cfd0c52..664f391 100644
--- a/cmd/config-validator/README.md
+++ b/cmd/config-validator/README.md
@@ -42,9 +42,6 @@ Validate a configuration file.
 
 # Validate with verbose output
 ./config-validator validate -config .copier/workflows/config.yaml -v
-
-# Validate legacy JSON config
-./config-validator validate -config config.json
 ```
 
 **Output:**
@@ -185,7 +182,7 @@ When files aren't matching your pattern:
 
 1. **Get actual file paths from logs:**
    ```bash
-   grep "sample file path" logs/app.log
+   # Check stdout for "sample file path" entries
    ```
 
 2. **Test your pattern:**
@@ -235,19 +232,6 @@ Before deploying a new configuration:
   -vars "lang=go,file=main.go"
 ```
 
-### Migrating from JSON to YAML
-
-```bash
-# Validate
-./config-validator validate -config workflow-config.yaml -v
-
-# Test patterns
-./config-validator test-pattern \
-  -type prefix \
-  -pattern "examples/" \
-  -file "examples/go/main.go"
-```
-
 ## Exit Codes
 
 - `0` - Success
diff --git a/cmd/config-validator/main.go b/cmd/config-validator/main.go
index 9c3eee7..45a3c54 100644
--- a/cmd/config-validator/main.go
+++ b/cmd/config-validator/main.go
@@ -93,7 +93,7 @@ func printUsage() {
 }
 
 func validateConfig(configFile string, verbose bool) {
-	content, err := os.ReadFile(configFile)
+	content, err := os.ReadFile(configFile) // #nosec G304 -- CLI tool, path from user arg
 	if err != nil {
 		fmt.Printf("❌ Error reading config file: %v\n", err)
 		os.Exit(1)
@@ -187,35 +187,73 @@ func testTransform(source, template, varsStr string) {
 }
 
 func initConfig(templateName, output string) {
-	// Simple workflow config template
-	template := `# Workflow Configuration
-# This file defines workflows for copying code examples between repositories
+	templates := map[string]string{
+		"basic": `# Workflow Configuration — Basic (move transformation)
+# This file defines workflows for copying code examples between repositories.
 
 workflows:
   - name: "example-workflow"
-    source:
-      repo: "mongodb/source-repo"
-      branch: "main"
-      path: "examples"
+    # source.repo and source.branch are inherited from the workflow config reference
     destination:
-      repo: "mongodb/dest-repo"
+      repo: "your-org/dest-repo"
       branch: "main"
     transformations:
       - move:
           from: "examples"
           to: "code-examples"
     commit_strategy:
-      type: "pr"
+      type: "pull_request"
       pr_title: "Update code examples"
       pr_body: "Automated update from source repository"
-`
+`,
+		"glob": `# Workflow Configuration — Glob transformation
+# Uses glob patterns for flexible file matching.
+
+workflows:
+  - name: "copy-go-examples"
+    destination:
+      repo: "your-org/dest-repo"
+      branch: "main"
+    transformations:
+      - glob:
+          pattern: "examples/**/*.go"
+          transform: "code/${relative_path}"
+    commit_strategy:
+      type: "pull_request"
+      pr_title: "Update Go examples"
+      auto_merge: false
+`,
+		"regex": `# Workflow Configuration — Regex transformation
+# Uses regex with named capture groups for precise path control.
+
+workflows:
+  - name: "organize-by-language"
+    destination:
+      repo: "your-org/dest-repo"
+      branch: "main"
+    transformations:
+      - regex:
+          pattern: "^examples/(?P<lang>[^/]+)/(?P<file>.+)$"
+          transform: "code/${lang}/${file}"
+    commit_strategy:
+      type: "pull_request"
+      pr_title: "Update ${lang} examples"
+      auto_merge: false
+`,
+	}
+
+	tmpl, ok := templates[templateName]
+	if !ok {
+		fmt.Printf("❌ Unknown template: %s (must be basic, glob, or regex)\n", templateName)
+		os.Exit(1)
+	}
 
-	err := os.WriteFile(output, []byte(template), 0644)
+	err := os.WriteFile(output, []byte(tmpl), 0644) // #nosec G306 -- config template file, 0644 is intentional
 	if err != nil {
 		fmt.Printf("❌ Error writing config file: %v\n", err)
 		os.Exit(1)
 	}
 
-	fmt.Printf("✅ Created workflow config file: %s\n", output)
+	fmt.Printf("✅ Created workflow config file: %s (template: %s)\n", output, templateName)
 	fmt.Println("Edit this file to configure your workflows")
 }
diff --git a/cmd/test-pem/README.md b/cmd/test-pem/README.md
new file mode 100644
index 0000000..2fd02ce
--- /dev/null
+++ b/cmd/test-pem/README.md
@@ -0,0 +1,61 @@
+# test-pem
+
+Verify a GitHub App PEM private key by generating a JWT and calling the GitHub `/app` endpoint.
+
+## Purpose
+
+Quickly confirm that:
+
+- The PEM file is valid and correctly formatted (PKCS#1 or PKCS#8)
+- The App ID matches the key
+- GitHub accepts the resulting JWT
+
+## Build
+
+```bash
+go build -o test-pem ./cmd/test-pem
+```
+
+## Usage
+
+```bash
+./test-pem <pem-file> <app-id>
+```
+
+**Arguments:**
+
+| Argument  | Description                        |
+|-----------|------------------------------------|
+| pem-file  | Path to the `.pem` private key     |
+| app-id    | GitHub App ID (numeric)            |
+
+## Example
+
+```bash
+$ ./test-pem github-app.pem 123456
+✓ Read PEM file: github-app.pem (1674 bytes)
+✓ Parsed RSA private key (size: 2048 bits)
+✓ Generated JWT for App ID 123456
+
+Contacting GitHub API...
+Status: 200
+✅ Authentication successful!
+
+App info:
+{"id":123456,"slug":"my-app","name":"My App",...}
+```
+
+## Troubleshooting
+
+| Error | Cause | Fix |
+|-------|-------|-----|
+| `Failed to read PEM file` | File not found or unreadable | Check path and permissions |
+| `Failed to parse RSA private key` | Not a valid PEM key | Re-download from GitHub App settings |
+| `HTTP 401` | App ID doesn't match key, or key is revoked | Verify App ID; regenerate key if needed |
+
+## Exit Codes
+
+| Code | Meaning |
+|------|---------|
+| 0    | Authentication succeeded |
+| 1    | Any error (file, parse, network, auth) |
diff --git a/cmd/test-pem/main.go b/cmd/test-pem/main.go
new file mode 100644
index 0000000..6c59857
--- /dev/null
+++ b/cmd/test-pem/main.go
@@ -0,0 +1,97 @@
+// test-pem verifies a GitHub App PEM private key by generating a JWT
+// and calling the GitHub API's /app endpoint. This confirms the key
+// is valid, correctly formatted, and matches the App ID.
+package main
+
+import (
+	"crypto/rsa"
+	"fmt"
+	"io"
+	"net/http"
+	"os"
+	"time"
+
+	"github.com/golang-jwt/jwt/v5"
+)
+
+func main() {
+	if len(os.Args) < 3 {
+		fmt.Fprintf(os.Stderr, `test-pem — verify a GitHub App PEM key
+
+Usage: test-pem <pem-file> <app-id>
+
+Arguments:
+  pem-file  Path to the .pem private key file
+  app-id    GitHub App ID (numeric)
+
+Example:
+  test-pem github-app.pem 123456
+`)
+		os.Exit(1)
+	}
+
+	pemPath := os.Args[1]
+	appID := os.Args[2]
+
+	pemData, err := os.ReadFile(pemPath) // #nosec G304 -- CLI tool, path from user arg
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "❌ Failed to read PEM file %q: %v\n", pemPath, err)
+		os.Exit(1)
+	}
+	fmt.Printf("✓ Read PEM file: %s (%d bytes)\n", pemPath, len(pemData))
+
+	privateKey, err := jwt.ParseRSAPrivateKeyFromPEM(pemData)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "❌ Failed to parse RSA private key: %v\n", err)
+		fmt.Fprintf(os.Stderr, "  Ensure the file is a valid PKCS#1 or PKCS#8 PEM-encoded RSA key.\n")
+		os.Exit(1)
+	}
+	fmt.Printf("✓ Parsed RSA private key (size: %d bits)\n", privateKey.N.BitLen())
+
+	token, err := generateJWT(appID, privateKey)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "❌ Failed to generate JWT: %v\n", err)
+		os.Exit(1)
+	}
+	fmt.Printf("✓ Generated JWT for App ID %s\n", appID)
+
+	req, err := http.NewRequest("GET", "https://api.github.com/app", nil)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "❌ Failed to create request: %v\n", err)
+		os.Exit(1)
+	}
+	req.Header.Set("Authorization", "Bearer "+token)
+	req.Header.Set("Accept", "application/vnd.github+json")
+
+	fmt.Println("\nContacting GitHub API...")
+	resp, err := http.DefaultClient.Do(req)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "❌ API request failed: %v\n", err)
+		os.Exit(1)
+	}
+	defer func() { _ = resp.Body.Close() }()
+
+	body, err := io.ReadAll(resp.Body)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "❌ Failed to read response: %v\n", err)
+		os.Exit(1)
+	}
+
+	fmt.Printf("Status: %d\n", resp.StatusCode)
+	if resp.StatusCode == http.StatusOK {
+		fmt.Printf("✅ Authentication successful!\n\nApp info:\n%s\n", body)
+	} else {
+		fmt.Fprintf(os.Stderr, "❌ Authentication failed (HTTP %d)\n%s\n", resp.StatusCode, body)
+		os.Exit(1)
+	}
+}
+
+func generateJWT(appID string, pk *rsa.PrivateKey) (string, error) {
+	now := time.Now()
+	claims := jwt.MapClaims{
+		"iat": now.Unix(),
+		"exp": now.Add(10 * time.Minute).Unix(),
+		"iss": appID,
+	}
+	return jwt.NewWithClaims(jwt.SigningMethodRS256, claims).SignedString(pk)
+}
diff --git a/cmd/test-webhook/README.md b/cmd/test-webhook/README.md
index 10070bf..6903385 100644
--- a/cmd/test-webhook/README.md
+++ b/cmd/test-webhook/README.md
@@ -31,7 +31,7 @@ Send a pre-made example payload to the webhook endpoint.
 
 **Options:**
 - `-payload` - Path to JSON payload file (required)
-- `-url` - Webhook URL (default: `http://localhost:8080/webhook`)
+- `-url` - Webhook URL (default: `http://localhost:8080/events`)
 
 **Example:**
 
@@ -41,7 +41,7 @@ Send a pre-made example payload to the webhook endpoint.
 
 # Use custom URL
 ./test-webhook -payload testdata/example-pr-merged.json \
-  -url http://localhost:8080/webhook
+  -url http://localhost:8080/events
 ```
 
 **Output:**
@@ -68,7 +68,7 @@ Fetch real PR data from GitHub and send it to the webhook.
 - `-pr` - Pull request number (required)
 - `-owner` - Repository owner (required)
 - `-repo` - Repository name (required)
-- `-url` - Webhook URL (default: `http://localhost:8080/webhook`)
+- `-url` - Webhook URL (default: `http://localhost:8080/events`)
 
 **Environment Variables:**
 - `GITHUB_TOKEN` - GitHub personal access token (required for real PR data)
@@ -84,7 +84,7 @@ export GITHUB_TOKEN=ghp_your_token_here
 
 # Test with custom URL
 ./test-webhook -pr 42 -owner mongodb -repo docs-code-examples \
-  -url http://localhost:8080/webhook
+  -url http://localhost:8080/events
 ```
 
 **Output:**
@@ -108,13 +108,12 @@ Test your configuration locally before deploying:
 
 ```bash
 # 1. Start app in dry-run mode
-DRY_RUN=true make run-local-quick
+./scripts/run-local.sh
 
 # 2. In another terminal, send test webhook
 ./test-webhook -payload testdata/example-pr-merged.json
 
-# 3. Check logs
-tail -f logs/app.log
+# 3. Check logs (JSON format on stdout via slog)
 ```
 
 ### Testing Pattern Matching
@@ -123,7 +122,7 @@ Test if your patterns match real PR files:
 
 ```bash
 # 1. Start app
-make run-local-quick
+./scripts/run-local.sh
 
 # 2. Send webhook with real PR data
 export GITHUB_TOKEN=ghp_...
@@ -145,7 +144,7 @@ DRY_RUN=true ./github-copier &
 ./test-webhook -payload testdata/example-pr-merged.json
 
 # 3. Check logs for transformed paths
-grep "transformed path" logs/app.log
+# Check stdout for "transformed path" entries
 ```
 
 ### Testing Slack Notifications
@@ -176,7 +175,7 @@ export LOG_LEVEL=debug
 ./test-webhook -payload testdata/example-pr-merged.json
 
 # 3. Review detailed logs
-grep "DEBUG" logs/app.log
+# Run with LOG_LEVEL=debug for verbose output
 ```
 
 ## Example Payloads
@@ -247,7 +246,7 @@ export GITHUB_TOKEN=ghp_...
 ./test-webhook -pr 42 -owner myorg -repo myrepo
 
 # 5. Review logs
-grep "matched" logs/app.log
+# Check stdout for "matched" entries
 ```
 
 ## Troubleshooting
@@ -286,8 +285,8 @@ Response: 404 Not Found
 
 **Solution:** Check the webhook URL:
 ```bash
-# Default is /webhook
-./test-webhook -payload test.json -url http://localhost:8080/webhook
+# Default is /events
+./test-webhook -payload test.json -url http://localhost:8080/events
 ```
 
 ### GitHub API Rate Limit
@@ -364,37 +363,6 @@ chmod +x run-tests.sh
 ./run-tests.sh
 ```
 
-### Integration with CI/CD
-
-```yaml
-# .github/workflows/test.yml
-name: Test Examples Copier
-
-on: [push, pull_request]
-
-jobs:
-  test:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      
-      - name: Set up Go
-        uses: actions/setup-go@v2
-        with:
-          go-version: 1.23.4
-      
-      - name: Build
-        run: |
-          go build -o github-copier .
-          go build -o test-webhook ./cmd/test-webhook
-      
-      - name: Test
-        run: |
-          DRY_RUN=true ./github-copier &
-          sleep 2
-          ./test-webhook -payload testdata/example-pr-merged.json
-```
-
 ## Exit Codes
 
 - `0` - Success
@@ -405,5 +373,4 @@ jobs:
 - [Webhook Testing Guide](../../docs/WEBHOOK-TESTING.md) - Comprehensive testing guide
 - [Local Testing](../../docs/LOCAL-TESTING.md) - Local development
 - [Test Payloads](../../testdata/README.md) - Example payloads
-- [Quick Reference](../../QUICK-REFERENCE.md) - All commands
 
diff --git a/cmd/test-webhook/main.go b/cmd/test-webhook/main.go
index a84c3b8..d240cb4 100644
--- a/cmd/test-webhook/main.go
+++ b/cmd/test-webhook/main.go
@@ -12,7 +12,8 @@ import (
 	"net/http"
 	"os"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
+	"github.com/google/uuid"
 )
 
 func main() {
@@ -38,7 +39,7 @@ func main() {
 
 	// Option 1: Use custom payload file
 	if *payloadFile != "" {
-		payload, err = os.ReadFile(*payloadFile)
+		payload, err = os.ReadFile(*payloadFile) // #nosec G304 -- CLI tool, path from user flag
 		if err != nil {
 			fmt.Printf("Error reading payload file: %v\n", err)
 			os.Exit(1)
@@ -117,7 +118,7 @@ Examples:
 
   # Send to production with secret
   test-webhook -pr 123 -owner myorg -repo myrepo \
-    -url https://myapp.appspot.com/events \
+    -url https://your-service.run.app/events \
     -secret "my-webhook-secret"
 
 Environment Variables:
@@ -147,7 +148,7 @@ func fetchPRPayload(owner, repo string, prNumber int) ([]byte, error) {
 	if err != nil {
 		return nil, err
 	}
-	defer resp.Body.Close()
+	defer func() { _ = resp.Body.Close() }()
 
 	if resp.StatusCode != 200 {
 		body, _ := io.ReadAll(resp.Body)
@@ -173,7 +174,7 @@ func fetchPRPayload(owner, repo string, prNumber int) ([]byte, error) {
 	if err != nil {
 		return nil, err
 	}
-	defer filesResp.Body.Close()
+	defer func() { _ = filesResp.Body.Close() }()
 
 	var files []map[string]interface{}
 	if err := json.NewDecoder(filesResp.Body).Decode(&files); err != nil {
@@ -185,9 +186,9 @@ func fetchPRPayload(owner, repo string, prNumber int) ([]byte, error) {
 		"action": "closed",
 		"number": prNumber,
 		"pull_request": map[string]interface{}{
-			"number":       pr.GetNumber(),
-			"state":        pr.GetState(),
-			"merged":       pr.GetMerged(),
+			"number":           pr.GetNumber(),
+			"state":            pr.GetState(),
+			"merged":           pr.GetMerged(),
 			"merge_commit_sha": pr.GetMergeCommitSHA(),
 			"head": map[string]interface{}{
 				"ref": pr.GetHead().GetRef(),
@@ -223,9 +224,9 @@ func createExamplePayload() []byte {
 		"action": "closed",
 		"number": 42,
 		"pull_request": map[string]interface{}{
-			"number": 42,
-			"state":  "closed",
-			"merged": true,
+			"number":           42,
+			"state":            "closed",
+			"merged":           true,
 			"merge_commit_sha": "abc123def456",
 			"head": map[string]interface{}{
 				"ref": "feature-branch",
@@ -265,6 +266,11 @@ func sendWebhook(url string, payload []byte, secret string) error {
 	req.Header.Set("Content-Type", "application/json")
 	req.Header.Set("X-GitHub-Event", "pull_request")
 
+	// Add unique delivery ID for idempotency tracking
+	deliveryID := uuid.New().String()
+	req.Header.Set("X-GitHub-Delivery", deliveryID)
+	fmt.Printf("✓ Delivery ID: %s\n", deliveryID)
+
 	// Add signature if secret provided
 	if secret != "" {
 		signature := generateSignature(payload, secret)
@@ -277,7 +283,7 @@ func sendWebhook(url string, payload []byte, secret string) error {
 	if err != nil {
 		return err
 	}
-	defer resp.Body.Close()
+	defer func() { _ = resp.Body.Close() }()
 
 	body, _ := io.ReadAll(resp.Body)
 
@@ -298,4 +304,3 @@ func generateSignature(payload []byte, secret string) string {
 	mac.Write(payload)
 	return "sha256=" + hex.EncodeToString(mac.Sum(nil))
 }
-
diff --git a/configs/.env.local.example b/configs/.env.local.example
index 01656ae..bc5ba7b 100644
--- a/configs/.env.local.example
+++ b/configs/.env.local.example
@@ -3,13 +3,13 @@
 # To use this file, copy it to .env and edit with your values:
 #   cp configs/.env.local configs/.env
 #   source configs/.env
-#   ./examples-copier
+#   ./github-copier
 
 # Or use with make:
 #   make run-dry
 
 # Or run directly:
-#   COPIER_DISABLE_CLOUD_LOGGING=true DRY_RUN=true ./examples-copier
+#   COPIER_DISABLE_CLOUD_LOGGING=true DRY_RUN=true ./github-copier
 
 # ============================================================================
 # REQUIRED FOR LOCAL TESTING
@@ -54,27 +54,36 @@ METRICS_ENABLED=true
 PORT=8080
 
 # ============================================================================
-# GITHUB CREDENTIALS (REQUIRED FOR REAL PR TESTING)
+# GITHUB APP CREDENTIALS (REQUIRED — the app authenticates on startup)
 # ============================================================================
 
-# GitHub App ID (get from GitHub App settings)
-# GITHUB_APP_ID=123456
+# GitHub App ID and Installation ID (get from GitHub App settings)
+GITHUB_APP_ID=
+INSTALLATION_ID=
 
-# GitHub Installation ID (get from GitHub App installation)
-# GITHUB_INSTALLATION_ID=789012
+# --- PEM Key: choose ONE of the options below ---
 
-# For local testing, you can use a Personal Access Token instead
-# Get from: https://github.com/settings/tokens
-# Required scopes: repo (for reading PRs and files)
-GITHUB_TOKEN=
+# Option A: Fetch PEM from GCP Secret Manager (requires: gcloud auth application-default login)
+#   Just leave SKIP_SECRET_MANAGER unset. The app reads the secret named in PEM_NAME
+#   (default: CODE_COPIER_PEM) from your GOOGLE_CLOUD_PROJECT_ID.
+# PEM_NAME=CODE_COPIER_PEM
+# GOOGLE_CLOUD_PROJECT_ID=github-copy-code-examples
+
+# Option B: Provide the PEM key directly (no GCP access needed)
+#   Set SKIP_SECRET_MANAGER=true and provide the key via one of:
+# SKIP_SECRET_MANAGER=true
+# GITHUB_APP_PRIVATE_KEY_B64=<output of: base64 -i /path/to/your-key.pem>
+#   Or inline (replace newlines with \n):
+# GITHUB_APP_PRIVATE_KEY="-----BEGIN RSA PRIVATE KEY-----\n...\n-----END RSA PRIVATE KEY-----"
 
 # ============================================================================
-# OPTIONAL: GOOGLE CLOUD (ONLY IF TESTING CLOUD FEATURES)
+# OPTIONAL: GITHUB TOKEN (for test-webhook CLI / test-with-pr.sh only)
 # ============================================================================
 
-# Only set these if you want to test with actual GCP
-# GCP_PROJECT_ID=your-project-id
-# PEM_KEY_NAME=projects/123/secrets/CODE_COPIER_PEM/versions/latest
+# A PAT is NOT used by the app itself — only by the test-webhook CLI tool
+# to fetch real PR data from the GitHub API.
+# Get from: https://github.com/settings/tokens (scope: repo)
+GITHUB_TOKEN=
 
 # ============================================================================
 # OPTIONAL: MONGODB AUDIT LOGGING (FOR LOCAL TESTING)
@@ -108,7 +117,7 @@ SLACK_WEBHOOK_URL=
 SLACK_CHANNEL=#code-examples
 
 # Slack bot username (default: Examples Copier)
-SLACK_USERNAME=Examples Copier
+SLACK_USERNAME=GitHub Copier
 
 # Slack bot icon emoji (default: :robot_face:)
 SLACK_ICON_EMOJI=:robot_face:
@@ -168,7 +177,7 @@ SLACK_ENABLED=false
 #
 # 6. TESTING:
 #    - Use CONFIG_FILE="copier-config.example.yaml" for testing
-#    - Set WEBSERVER_PATH="/events" to match GitHub webhook
+#    - WEBSERVER_PATH defaults to "/events" to match GitHub webhook
 #    - Use PORT="3000" or any available port
 
 # =============================================================================
diff --git a/configs/README.md b/configs/README.md
index 5a4ab16..953e0fe 100644
--- a/configs/README.md
+++ b/configs/README.md
@@ -101,35 +101,13 @@ env_variables:
 
 ---
 
-## Deployment Targets
+## Deployment Target
 
-This service supports **two Google Cloud deployment options**:
+This service deploys to **Google Cloud Run**.
 
-### App Engine (Flexible Environment)
+### Cloud Run
 
-**Config file:** `env.yaml` (with `env_variables:` wrapper)
-
-**Format:**
-```yaml
-env_variables:
-  GITHUB_APP_ID: "123456"
-  REPO_OWNER: "mongodb"
-```
-
-**Deploy:**
-```bash
-cp configs/env.yaml.production env.yaml
-# Edit env.yaml with your values
-gcloud app deploy app.yaml  # Includes env.yaml automatically
-```
-
-**Best for:** Long-running services, always-on applications
-
----
-
-### Cloud Run (Serverless Containers)
-
-**Config file:** `env-cloudrun.yaml` (plain YAML, no wrapper)
+**Config file:** `env-cloudrun.yaml` (plain YAML key-value pairs)
 
 **Format:**
 ```yaml
@@ -140,13 +118,10 @@ REPO_OWNER: "mongodb"
 **Deploy:**
 ```bash
 cp configs/env.yaml.production env-cloudrun.yaml
-# Remove the 'env_variables:' wrapper
 # Edit env-cloudrun.yaml with your values
-gcloud run deploy github-copier --source . --env-vars-file=env-cloudrun.yaml
+./scripts/deploy-cloudrun.sh
 ```
 
-**Best for:** Cost-effective, scales to zero, serverless
-
 ---
 
 ## Usage Scenarios
@@ -157,10 +132,10 @@ gcloud run deploy github-copier --source . --env-vars-file=env-cloudrun.yaml
 
 ```bash
 # Quick start
-cp configs/env.yaml.production env.yaml
-nano env.yaml  # Update PROJECT_NUMBER and values
+cp configs/env.yaml.production env-cloudrun.yaml
+nano env-cloudrun.yaml  # Update PROJECT_NUMBER and values
 ./scripts/grant-secret-access.sh
-gcloud app deploy app.yaml  # env.yaml is included via 'includes' directive
+./scripts/deploy-cloudrun.sh
 ```
 
 **Why:** Pre-configured with production best practices, minimal setup required.
@@ -216,7 +191,7 @@ nano env.yaml
 # - Set custom defaults
 
 # Deploy
-gcloud app deploy app.yaml  # env.yaml is included via 'includes' directive
+./scripts/deploy-cloudrun.sh
 ```
 
 **Why:** Need advanced features not in production template.
@@ -240,22 +215,9 @@ Or manually convert:
 GITHUB_APP_ID=123456
 REPO_OWNER=mongodb
 
-# env.yaml format:
-env_variables:
-  GITHUB_APP_ID: "123456"
-  REPO_OWNER: "mongodb"
-```
-
-### Between App Engine and Cloud Run formats
-
-Use the format conversion script:
-
-```bash
-# Convert App Engine → Cloud Run
-./scripts/convert-env-format.sh to-cloudrun env.yaml env-cloudrun.yaml
-
-# Convert Cloud Run → App Engine
-./scripts/convert-env-format.sh to-appengine env-cloudrun.yaml env.yaml
+# Cloud Run YAML format:
+GITHUB_APP_ID: "123456"
+REPO_OWNER: "mongodb"
 ```
 
 **Key difference:**
@@ -337,7 +299,6 @@ github-copier/
 
 ## See Also
 
-- [CONFIGURATION-GUIDE.md](../docs/CONFIGURATION-GUIDE.md) - Variable validation and reference
 - [DEPLOYMENT.md](../docs/DEPLOYMENT.md) - Complete deployment guide
 - [LOCAL-TESTING.md](../docs/LOCAL-TESTING.md) - Local development guide
 
diff --git a/configs/copier-config-examples/SOURCE-REPO-README.md b/configs/copier-config-examples/SOURCE-REPO-README.md
index b48b54c..c1f5240 100644
--- a/configs/copier-config-examples/SOURCE-REPO-README.md
+++ b/configs/copier-config-examples/SOURCE-REPO-README.md
@@ -24,7 +24,7 @@ This directory contains workflow configurations for automatically copying code e
 
 **Where are the logs?**
 ```bash
-gcloud app logs read --limit=100 | grep "your-repo-name"
+gcloud run services logs read github-copier --limit=100
 ```
 
 ## Quick Start
@@ -455,14 +455,8 @@ workflows:
 ### How do I view the logs?
 
 ```bash
-# View recent logs
-gcloud app logs read --limit=100
-
-# Search for your PR
-gcloud app logs read --limit=200 | grep "PR #123"
-
-# Search for your repo
-gcloud app logs read --limit=200 | grep "your-repo-name"
+# View recent logs (Cloud Run)
+gcloud run services logs read github-copier --limit=100
 ```
 
 ### How do I test my configuration?
diff --git a/configs/environment.go b/configs/environment.go
index bf9ff1f..bf6aac3 100644
--- a/configs/environment.go
+++ b/configs/environment.go
@@ -75,9 +75,9 @@ const (
 	DeprecationFile            = "DEPRECATION_FILE"
 	WebserverPath              = "WEBSERVER_PATH"
 	ConfigRepoBranch           = "CONFIG_REPO_BRANCH"
-	PEMKeyName                 = "PEM_NAME"
-	WebhookSecretName          = "WEBHOOK_SECRET_NAME"
-	WebhookSecret              = "WEBHOOK_SECRET"
+	PEMKeyName                 = "PEM_NAME"            // #nosec G101 -- env var name, not a credential
+	WebhookSecretName          = "WEBHOOK_SECRET_NAME" // #nosec G101 -- env var name, not a credential
+	WebhookSecret              = "WEBHOOK_SECRET"      // #nosec G101 -- env var name, not a credential
 	CopierLogName              = "COPIER_LOG_NAME"
 	GoogleCloudProjectId       = "GOOGLE_CLOUD_PROJECT_ID"
 	DefaultRecursiveCopy       = "DEFAULT_RECURSIVE_COPY"
@@ -86,11 +86,11 @@ const (
 	DryRun                     = "DRY_RUN"
 	AuditEnabled               = "AUDIT_ENABLED"
 	MongoURI                   = "MONGO_URI"
-	MongoURISecretName         = "MONGO_URI_SECRET_NAME"
+	MongoURISecretName         = "MONGO_URI_SECRET_NAME" // #nosec G101 -- env var name, not a credential
 	AuditDatabase              = "AUDIT_DATABASE"
 	AuditCollection            = "AUDIT_COLLECTION"
 	MetricsEnabled             = "METRICS_ENABLED"
-	SlackWebhookURL            = "SLACK_WEBHOOK_URL"
+	SlackWebhookURL            = "SLACK_WEBHOOK_URL" // #nosec G101 -- env var name, not a credential
 	SlackChannel               = "SLACK_CHANNEL"
 	SlackUsername              = "SLACK_USERNAME"
 	SlackIconEmoji             = "SLACK_ICON_EMOJI"
@@ -109,19 +109,19 @@ func NewConfig() *Config {
 		CommitterEmail:             "bot@example.com",
 		ConfigFile:                 "copier-config.yaml",
 		DeprecationFile:            "deprecated_examples.json",
-		WebserverPath:              "/webhook",
-		ConfigRepoBranch:           "main",                                                           // Default branch to fetch config file from
-		PEMKeyName:                 "projects/1054147886816/secrets/CODE_COPIER_PEM/versions/latest", // default secret name for GCP Secret Manager
-		WebhookSecretName:          "projects/1054147886816/secrets/webhook-secret/versions/latest",  // default webhook secret name for GCP Secret Manager
-		CopierLogName:              "copy-copier-log",                                                // default log name for logging to GCP
-		GoogleCloudProjectId:       "github-copy-code-examples",                                      // default project ID for logging to GCP
-		DefaultRecursiveCopy:       true,                                                             // system-wide default for recursive copying that individual config entries can override.
-		DefaultPRMerge:             false,                                                            // system-wide default for PR merge without review that individual config entries can override.
-		DefaultCommitMessage:       "Automated PR with updated examples",                             // default commit message used when per-config commit_message is absent.
-		GitHubAPIMaxRetries:        3,                                                                // default number of retry attempts for GitHub API calls
-		GitHubAPIInitialRetryDelay: 500,                                                              // default initial retry delay in milliseconds (exponential backoff)
-		PRMergePollMaxAttempts:     20,                                                               // default max attempts to poll PR for mergeability (~10 seconds with 500ms interval)
-		PRMergePollInterval:        500,                                                              // default polling interval in milliseconds
+		WebserverPath:              "/events",
+		ConfigRepoBranch:           "main",                               // Default branch to fetch config file from
+		PEMKeyName:                 "CODE_COPIER_PEM",                    // short secret name; resolved to full path at runtime via SecretPath()
+		WebhookSecretName:          "webhook-secret",                     // short secret name; resolved to full path at runtime via SecretPath()
+		CopierLogName:              "copy-copier-log",                    // default log name for logging to GCP
+		GoogleCloudProjectId:       "github-copy-code-examples",          // default project ID for logging to GCP
+		DefaultRecursiveCopy:       true,                                 // system-wide default for recursive copying that individual config entries can override.
+		DefaultPRMerge:             false,                                // system-wide default for PR merge without review that individual config entries can override.
+		DefaultCommitMessage:       "Automated PR with updated examples", // default commit message used when per-config commit_message is absent.
+		GitHubAPIMaxRetries:        3,                                    // default number of retry attempts for GitHub API calls
+		GitHubAPIInitialRetryDelay: 500,                                  // default initial retry delay in milliseconds (exponential backoff)
+		PRMergePollMaxAttempts:     20,                                   // default max attempts to poll PR for mergeability (~10 seconds with 500ms interval)
+		PRMergePollInterval:        500,                                  // default polling interval in milliseconds
 	}
 }
 
@@ -203,28 +203,6 @@ func LoadEnvironment(envFile string) (*Config, error) {
 	config.PRMergePollMaxAttempts = getIntEnvWithDefault(PRMergePollMaxAttempts, config.PRMergePollMaxAttempts)
 	config.PRMergePollInterval = getIntEnvWithDefault(PRMergePollInterval, config.PRMergePollInterval)
 
-	// Export resolved values back into environment so downstream os.Getenv sees defaults
-	_ = os.Setenv(Port, config.Port)
-	_ = os.Setenv(ConfigRepoName, config.ConfigRepoName)
-	_ = os.Setenv(ConfigRepoOwner, config.ConfigRepoOwner)
-	_ = os.Setenv(AppId, config.AppId)
-	_ = os.Setenv(AppClientId, config.AppClientId)
-	_ = os.Setenv(InstallationId, config.InstallationId)
-	_ = os.Setenv(CommitterName, config.CommitterName)
-	_ = os.Setenv(CommitterEmail, config.CommitterEmail)
-	_ = os.Setenv(ConfigFile, config.ConfigFile)
-	_ = os.Setenv(MainConfigFile, config.MainConfigFile)
-	_ = os.Setenv(UseMainConfig, fmt.Sprintf("%t", config.UseMainConfig))
-	_ = os.Setenv(DeprecationFile, config.DeprecationFile)
-	_ = os.Setenv(WebserverPath, config.WebserverPath)
-	_ = os.Setenv(ConfigRepoBranch, config.ConfigRepoBranch)
-	_ = os.Setenv(PEMKeyName, config.PEMKeyName)
-	_ = os.Setenv(CopierLogName, config.CopierLogName)
-	_ = os.Setenv(GoogleCloudProjectId, config.GoogleCloudProjectId)
-	_ = os.Setenv(DefaultRecursiveCopy, fmt.Sprintf("%t", config.DefaultRecursiveCopy))
-	_ = os.Setenv(DefaultPRMerge, fmt.Sprintf("%t", config.DefaultPRMerge))
-	_ = os.Setenv(DefaultCommitMessage, config.DefaultCommitMessage)
-
 	if err := validateConfig(config); err != nil {
 		return nil, err
 	}
@@ -232,6 +210,16 @@ func LoadEnvironment(envFile string) (*Config, error) {
 	return config, nil
 }
 
+// SecretPath resolves a secret name to a fully-qualified GCP Secret Manager resource path.
+// If the name already contains "projects/", it is returned as-is (for backward compatibility).
+// Otherwise, it builds the full path using the configured GoogleCloudProjectId.
+func (c *Config) SecretPath(secretName string) string {
+	if strings.HasPrefix(secretName, "projects/") {
+		return secretName
+	}
+	return fmt.Sprintf("projects/%s/secrets/%s/versions/latest", c.GoogleCloudProjectId, secretName)
+}
+
 // getEnvWithDefault returns the environment variable value or default if not set
 func getEnvWithDefault(key, defaultValue string) string {
 	value := os.Getenv(key)
@@ -284,5 +272,15 @@ func validateConfig(config *Config) error {
 		return fmt.Errorf("missing required environment variables: %s", strings.Join(missingVars, ", "))
 	}
 
+	// Warn if webhook secret is not configured.
+	// In production, webhook signature verification should always be enabled
+	// to prevent unauthorized requests from being processed.
+	env := getEnvWithDefault(EnvFile, "")
+	if config.WebhookSecret == "" && config.WebhookSecretName == "" {
+		if env == "production" || env == "prod" {
+			return fmt.Errorf("WEBHOOK_SECRET or WEBHOOK_SECRET_NAME is required in production to enable webhook signature verification")
+		}
+	}
+
 	return nil
 }
diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
index 32c29cb..924960d 100644
--- a/docs/ARCHITECTURE.md
+++ b/docs/ARCHITECTURE.md
@@ -581,19 +581,37 @@ auto_merge: false
 
 The application is designed for concurrent operations:
 
+- **TokenManager**: Thread-safe token state via `sync.RWMutex`
 - **FileStateService**: Thread-safe with `sync.RWMutex`
+- **DeliveryTracker**: Thread-safe webhook deduplication via `sync.Mutex`
 - **MetricsCollector**: Thread-safe counters
 - **AuditLogger**: Thread-safe MongoDB operations
 - **ServiceContainer**: Immutable after initialization
 
 ## Error Handling
 
+- Sentinel errors in `services/errors.go` (`ErrRateLimited`, `ErrNotFound`, etc.)
+- All errors wrapped with `%w` for `errors.Is()`/`errors.As()` compatibility
 - Context-aware cancellation support
 - Graceful degradation (audit logging optional)
-- Detailed error logging with full context
+- Structured error logging with full context via `log/slog`
 - Metrics tracking for failed operations
 - No-op implementations for optional features
 
+## Rate Limit Handling
+
+The `RateLimitTransport` (`services/rate_limit.go`) wraps the HTTP transport to automatically:
+- Detect 403/429 responses with `X-RateLimit-Remaining: 0` or `Retry-After` headers
+- Wait and retry with appropriate backoff
+- Log rate limit events with structured context
+
+## Webhook Idempotency
+
+The `DeliveryTracker` (`services/delivery_tracker.go`) prevents duplicate processing:
+- Tracks `X-GitHub-Delivery` header from each webhook
+- TTL-based cleanup to prevent unbounded memory growth
+- Returns 200 OK for already-processed deliveries
+
 ## Performance Considerations
 
 - **Batch Operations**: Multiple files committed in single operation
@@ -639,8 +657,9 @@ METRICS_ENABLED: "true"
 
 **Health Monitoring:**
 - `/health` endpoint for liveness checks
+- `/ready` endpoint for readiness probes (checks GitHub auth, rate limits, MongoDB)
 - `/metrics` endpoint for monitoring
-- Structured logs for analysis
+- Structured JSON logs via `log/slog` for analysis
 
 ## Future Enhancements
 
@@ -649,6 +668,4 @@ Potential improvements:
 1. **Automatic Cleanup PRs** - Create PRs to remove deprecated files from targets
 2. **Expiration Dates** - Auto-remove deprecation entries after X days
 3. **Config Validation CLI** - Enhanced validation tool
-4. **Retry Logic** - Automatic retry for failed GitHub API calls
-5. **Rate Limiting** - Respect GitHub API rate limits
 
diff --git a/docs/DEBUG-LOGGING.md b/docs/DEBUG-LOGGING.md
deleted file mode 100644
index 05f3682..0000000
--- a/docs/DEBUG-LOGGING.md
+++ /dev/null
@@ -1,376 +0,0 @@
-# Debug Logging Guide
-
-This guide explains how to enable and use debug logging in the Examples Copier application.
-
-## Overview
-
-The Examples Copier supports configurable logging levels to help with development, troubleshooting, and debugging. By default, the application logs at the INFO level, but you can enable DEBUG logging for more verbose output.
-
-## Environment Variables
-
-### LOG_LEVEL
-
-**Purpose:** Set the logging level for the application
-
-**Values:**
-- `info` (default) - Standard operational logs
-- `debug` - Verbose debug logs with detailed operation information
-
-**Example:**
-```bash
-LOG_LEVEL="debug"
-```
-
-### COPIER_DEBUG
-
-**Purpose:** Alternative way to enable debug mode
-
-**Values:**
-- `true` - Enable debug logging
-- `false` (default) - Standard logging
-
-**Example:**
-```bash
-COPIER_DEBUG="true"
-```
-
-**Note:** Either `LOG_LEVEL="debug"` OR `COPIER_DEBUG="true"` will enable debug logging. You only need to set one.
-
-### COPIER_DISABLE_CLOUD_LOGGING
-
-**Purpose:** Disable Google Cloud Logging (useful for local development)
-
-**Values:**
-- `true` - Disable GCP logging, only log to stdout
-- `false` (default) - Enable GCP logging if configured
-
-**Example:**
-```bash
-COPIER_DISABLE_CLOUD_LOGGING="true"
-```
-
-**Use case:** When developing locally, you may not want logs sent to Google Cloud. This flag keeps all logs local.
-
----
-
-## How It Works
-
-### Code Implementation
-
-The logging system is implemented in `services/logger.go`:
-
-```go
-// LogDebug writes debug logs only when LOG_LEVEL=debug or COPIER_DEBUG=true.
-func LogDebug(message string) {
-    if !isDebugEnabled() {
-        return
-    }
-    // Mirror to GCP as info if available, plus prefix to stdout
-    if googleInfoLogger != nil && gcpLoggingEnabled {
-        googleInfoLogger.Println("[DEBUG] " + message)
-    }
-    log.Println("[DEBUG] " + message)
-}
-
-func isDebugEnabled() bool {
-    if strings.EqualFold(os.Getenv("LOG_LEVEL"), "debug") {
-        return true
-    }
-    return strings.EqualFold(os.Getenv("COPIER_DEBUG"), "true")
-}
-
-func isCloudLoggingDisabled() bool {
-    return strings.EqualFold(os.Getenv("COPIER_DISABLE_CLOUD_LOGGING"), "true")
-}
-```
-
-### Log Levels
-
-The application supports the following log levels:
-
-| Level | Function | When to Use | Example |
-|-------|----------|-------------|---------|
-| **DEBUG** | `LogDebug()` | Detailed operation logs, file matching, API calls | `[DEBUG] Matched file: src/example.js` |
-| **INFO** | `LogInfo()` | Standard operational logs | `[INFO] Processing webhook event` |
-| **WARN** | `LogWarning()` | Warning conditions | `[WARN] File not found, skipping` |
-| **ERROR** | `LogError()` | Error conditions | `[ERROR] Failed to create PR` |
-| **CRITICAL** | `LogCritical()` | Critical failures | `[CRITICAL] Database connection failed` |
-
----
-
-## Usage Examples
-
-### Local Development with Debug Logging
-
-**Using .env file:**
-```bash
-# configs/.env
-LOG_LEVEL="debug"
-COPIER_DISABLE_CLOUD_LOGGING="true"
-DRY_RUN="true"
-```
-
-**Using environment variables:**
-```bash
-export LOG_LEVEL=debug
-export COPIER_DISABLE_CLOUD_LOGGING=true
-export DRY_RUN=true
-go run app.go
-```
-
-### Production with Debug Logging (Temporary)
-
-**env.yaml:**
-```yaml
-env_variables:
-  LOG_LEVEL: "debug"
-  # ... other variables
-```
-
-**Deploy:**
-```bash
-gcloud app deploy app.yaml  # env.yaml is included via 'includes' directive
-```
-
-**Important:** Remember to disable debug logging after troubleshooting to reduce log volume and costs.
-
-### Local Development without Cloud Logging
-
-```bash
-# configs/.env
-COPIER_DISABLE_CLOUD_LOGGING="true"
-```
-
-This keeps all logs local (stdout only), which is faster and doesn't require GCP credentials.
-
----
-
-## What Gets Logged at DEBUG Level?
-
-When debug logging is enabled, you'll see additional information about:
-
-### 1. **File Matching Operations**
-```
-[DEBUG] Checking pattern: src/**/*.js
-[DEBUG] Matched file: src/examples/example1.js
-[DEBUG] Excluded file: src/tests/test.js (matches exclude pattern)
-```
-
-### 2. **GitHub API Calls**
-```
-[DEBUG] Fetching file from GitHub: src/example.js
-[DEBUG] Creating PR for target repo: mongodb/docs-code-examples
-[DEBUG] GitHub API response: 200 OK
-```
-
-### 3. **Configuration Loading**
-```
-[DEBUG] Loading config file: copier-config.yaml
-[DEBUG] Found 5 copy rules
-[DEBUG] Rule 1: Copy src/**/*.js to examples/
-```
-
-### 4. **Webhook Processing**
-```
-[DEBUG] Received webhook event: pull_request
-[DEBUG] PR action: closed
-[DEBUG] PR merged: true
-[DEBUG] Processing 3 changed files
-```
-
-### 5. **Pattern Matching**
-```
-[DEBUG] Testing pattern: src/**/*.{js,ts}
-[DEBUG] File matches: true
-[DEBUG] Applying transformations: 2
-```
-
----
-
-## Best Practices
-
-### ✅ DO
-
-- **Enable debug logging when troubleshooting issues**
-  ```bash
-  LOG_LEVEL="debug"
-  ```
-
-- **Disable cloud logging for local development**
-  ```bash
-  COPIER_DISABLE_CLOUD_LOGGING="true"
-  ```
-
-- **Use debug logging with dry run mode for testing**
-  ```bash
-  LOG_LEVEL="debug"
-  DRY_RUN="true"
-  ```
-
-- **Disable debug logging in production after troubleshooting**
-  - High log volume can increase costs
-  - May expose sensitive information
-
-### ❌ DON'T
-
-- **Don't leave debug logging enabled in production long-term**
-  - Increases log volume and storage costs
-  - May impact performance
-  - Can expose internal implementation details
-
-- **Don't rely on debug logs for critical monitoring**
-  - Use INFO/WARN/ERROR levels for operational monitoring
-  - Debug logs may be disabled in production
-
-- **Don't log sensitive data even in debug mode**
-  - The code already avoids logging secrets
-  - Be careful when adding new debug logs
-
----
-
-## Troubleshooting
-
-### Debug Logs Not Appearing
-
-**Problem:** Set `LOG_LEVEL="debug"` but not seeing debug logs
-
-**Solutions:**
-
-1. **Check the variable is set correctly:**
-   ```bash
-   echo $LOG_LEVEL
-   # Should output: debug
-   ```
-
-2. **Try the alternative flag:**
-   ```bash
-   COPIER_DEBUG="true"
-   ```
-
-3. **Check case sensitivity:**
-   ```bash
-   # Both work (case-insensitive):
-   LOG_LEVEL="debug"
-   LOG_LEVEL="DEBUG"
-   ```
-
-4. **Verify the code is calling LogDebug():**
-   - Not all operations have debug logs
-   - Check `services/logger.go` for `LogDebug()` calls
-
-### Logs Not Going to Google Cloud
-
-**Problem:** Logs appear in stdout but not in Google Cloud Logging
-
-**Solutions:**
-
-1. **Check if cloud logging is disabled:**
-   ```bash
-   # Remove or set to false:
-   # COPIER_DISABLE_CLOUD_LOGGING="true"
-   ```
-
-2. **Verify GCP credentials:**
-   ```bash
-   gcloud auth application-default login
-   ```
-
-3. **Check project ID is set:**
-   ```bash
-   GOOGLE_CLOUD_PROJECT_ID="your-project-id"
-   ```
-
-4. **Check log name is set:**
-   ```bash
-   COPIER_LOG_NAME="code-copier-log"
-   ```
-
-### Too Many Logs
-
-**Problem:** Debug logging produces too much output
-
-**Solutions:**
-
-1. **Disable debug logging:**
-   ```bash
-   # Remove or comment out:
-   # LOG_LEVEL="debug"
-   # COPIER_DEBUG="true"
-   ```
-
-2. **Use grep to filter:**
-   ```bash
-   # Show only errors:
-   go run app.go 2>&1 | grep ERROR
-   
-   # Show only specific operations:
-   go run app.go 2>&1 | grep "pattern matching"
-   ```
-
-3. **Redirect to file:**
-   ```bash
-   go run app.go > debug.log 2>&1
-   ```
-
----
-
-## Configuration Examples
-
-### Example 1: Local Development (Recommended)
-
-```bash
-# configs/.env
-LOG_LEVEL="debug"
-COPIER_DISABLE_CLOUD_LOGGING="true"
-DRY_RUN="true"
-AUDIT_ENABLED="false"
-METRICS_ENABLED="true"
-```
-
-**Why:**
-- Debug logs help understand what's happening
-- No cloud logging keeps it fast and local
-- Dry run prevents accidental changes
-- No audit logging (simpler setup)
-
-### Example 2: Production Troubleshooting
-
-```yaml
-# env.yaml
-env_variables:
-  LOG_LEVEL: "debug"
-  GOOGLE_CLOUD_PROJECT_ID: "your-project-id"
-  COPIER_LOG_NAME: "code-copier-log"
-  # ... other variables
-```
-
-**Why:**
-- Temporarily enable debug for troubleshooting
-- Logs go to Cloud Logging for analysis
-- Remember to disable after fixing issue
-
-### Example 3: Local with Cloud Logging
-
-```bash
-# configs/.env
-LOG_LEVEL="debug"
-GOOGLE_CLOUD_PROJECT_ID="your-project-id"
-COPIER_LOG_NAME="code-copier-log-dev"
-# COPIER_DISABLE_CLOUD_LOGGING not set (defaults to false)
-```
-
-**Why:**
-- Test cloud logging integration locally
-- Separate log name for dev environment
-- Useful for testing logging infrastructure
-
----
-
-## See Also
-
-- [LOCAL-TESTING.md](LOCAL-TESTING.md) - Local development guide
-- [TROUBLESHOOTING.md](TROUBLESHOOTING.md) - General troubleshooting
-- [CONFIGURATION-GUIDE.md](CONFIGURATION-GUIDE.md) - Complete configuration reference
-- [../configs/env.yaml.example](../configs/env.yaml.example) - All environment variables
-- [../configs/.env.example](../configs/.env.example) - Local development template
-
diff --git a/docs/DEPLOYMENT.md b/docs/DEPLOYMENT.md
index b7d312d..8235616 100644
--- a/docs/DEPLOYMENT.md
+++ b/docs/DEPLOYMENT.md
@@ -18,7 +18,7 @@ Complete guide for deploying the GitHub Code Example Copier to Google Cloud Run
 
 ### Required Tools
 
-- **Go 1.23+** - For local development and testing
+- **Go 1.26+** - For local development and testing
 - **Google Cloud SDK** - For deployment
 - **GitHub App** - With appropriate permissions
 - **MongoDB Atlas** (optional) - For audit logging
@@ -432,7 +432,7 @@ curl ${SERVICE_URL}/health
    - Go to: `https://github.com/YOUR_ORG/YOUR_REPO/settings/hooks`
 
 2. **Add or edit webhook**
-   - **Payload URL:** `https://examples-copier-XXXXXXXXXX-uc.a.run.app/events` (use your Cloud Run URL)
+   - **Payload URL:** `https://YOUR_SERVICE_URL/events` (use your Cloud Run URL)
    - **Content type:** `application/json`
    - **Secret:** (the webhook secret from Secret Manager)
    - **Events:** Select "Pull requests"
@@ -451,7 +451,7 @@ curl ${SERVICE_URL}/health
 ```bash
 # Create and merge a test PR
 # Watch logs for webhook receipt
-gcloud app logs tail -s default | grep webhook
+gcloud run services logs read github-copier --limit=50
 ```
 
 **Option B: Redeliver from GitHub**
@@ -465,7 +465,7 @@ gcloud app logs tail -s default | grep webhook
 
 ```bash
 # Check logs for successful processing
-gcloud app logs read --limit=50
+gcloud run services logs read github-copier --limit=50
 
 # Look for:
 # ✅ "Starting web server on port :8080"
@@ -485,24 +485,18 @@ gcloud app logs read --limit=50
 ### View Logs
 
 ```bash
-# Real-time logs
-gcloud app logs tail -s default
-
 # Recent logs
-gcloud app logs read --limit=100
-
-# Filter for errors
-gcloud app logs read --limit=100 | grep ERROR
+gcloud run services logs read github-copier --limit=100
 
-# Filter for webhooks
-gcloud app logs read --limit=100 | grep webhook
+# Real-time log streaming
+gcloud beta run services logs tail github-copier
 ```
 
 ### Check Metrics
 
 ```bash
 # Metrics endpoint
-curl https://YOUR_APP.appspot.com/metrics
+curl https://YOUR_SERVICE_URL/metrics
 
 # Response includes:
 # - webhooks_received
@@ -616,7 +610,8 @@ cd github-copier
 
 ```bash
 PROJECT_NUMBER=$(gcloud projects describe $(gcloud config get-value project) --format="value(projectNumber)")
-SERVICE_ACCOUNT="${PROJECT_NUMBER}@appspot.gserviceaccount.com"
+# Use the Cloud Run service account (default compute, or a custom one)
+SERVICE_ACCOUNT="${PROJECT_NUMBER}-compute@developer.gserviceaccount.com"
 
 gcloud secrets add-iam-policy-binding CODE_COPIER_PEM \
   --member="serviceAccount:${SERVICE_ACCOUNT}" \
@@ -633,9 +628,9 @@ gcloud secrets add-iam-policy-binding mongo-uri \
 
 **Verify:**
 ```bash
-gcloud secrets get-iam-policy CODE_COPIER_PEM | grep @appspot
-gcloud secrets get-iam-policy webhook-secret | grep @appspot
-gcloud secrets get-iam-policy mongo-uri | grep @appspot
+gcloud secrets get-iam-policy CODE_COPIER_PEM | grep compute
+gcloud secrets get-iam-policy webhook-secret | grep compute
+gcloud secrets get-iam-policy mongo-uri | grep compute
 ```
 
 ### ☐ 5. Create env.yaml
@@ -673,27 +668,13 @@ grep "env.yaml" .gitignore
 echo "env.yaml" >> .gitignore
 ```
 
-### ☐ 7. Verify app.yaml Configuration
-
-```bash
-cat app.yaml
-```
-
-**Should contain:**
-```yaml
-runtime: go
-runtime_config:
-  operating_system: "ubuntu22"
-  runtime_version: "1.23"
-env: flex
-```
+### ☐ 7. Verify Dockerfile
 
-**Should NOT contain:**
-- ❌ `env_variables:` section (those go in env.yaml)
+Ensure the `Dockerfile` exists and is correctly configured. The app uses a multi-stage build with a non-root user and `HEALTHCHECK`.
 
 ---
 
-## 🚀 Deployment
+## Deployment
 
 ### ☐ 8. Deploy to Cloud Run
 
@@ -704,29 +685,18 @@ cd github-copier
 ./scripts/deploy-cloudrun.sh
 ```
 
-**Expected output:**
-```
-Updating service [default]...done.
-Setting traffic split for service [default]...done.
-Deployed service [default] to [https://YOUR_APP.appspot.com]
-```
-
 ### ☐ 9. Verify Deployment
 
 ```bash
-# Check versions
-gcloud app versions list
-
-# Get app URL
-APP_URL=$(gcloud app describe --format="value(defaultHostname)")
-echo "App URL: https://${APP_URL}"
+# Get service URL
+gcloud run services describe github-copier --format="value(status.url)"
 ```
 
 ### ☐ 10. Check Logs
 
 ```bash
-# View real-time logs
-gcloud app logs tail -s default
+# View recent logs
+gcloud run services logs read github-copier --limit=50
 ```
 
 **Look for:**
@@ -743,11 +713,14 @@ gcloud app logs tail -s default
 ### ☐ 11. Test Health Endpoint
 
 ```bash
-# Get app URL
-APP_URL=$(gcloud app describe --format="value(defaultHostname)")
+# Get service URL
+SERVICE_URL=$(gcloud run services describe github-copier --format="value(status.url)")
 
-# Test health
-curl https://${APP_URL}/health
+# Test health (liveness)
+curl ${SERVICE_URL}/health
+
+# Test readiness
+curl ${SERVICE_URL}/ready
 ```
 
 **Expected response:**
@@ -786,7 +759,7 @@ gcloud secrets versions access latest --secret=webhook-secret
     - URL: `https://github.com/YOUR_ORG/YOUR_REPO/settings/hooks`
 
 2. **Add or edit webhook**
-    - **Payload URL:** `https://YOUR_APP.appspot.com/events`
+    - **Payload URL:** `https://YOUR_SERVICE_URL/events`
     - **Content type:** `application/json`
     - **Secret:** (paste the value from step 12)
     - **SSL verification:** Enable SSL verification
@@ -810,18 +783,18 @@ gcloud secrets versions access latest --secret=webhook-secret
 
 ```bash
 # Watch logs
-gcloud app logs tail -s default | grep webhook
+gcloud run services logs read github-copier --limit=50
 ```
 
 ---
 
-## ✅ Post-Deployment Verification
+## Post-Deployment Verification
 
 ### ☐ 15. Verify Secrets Loaded
 
 ```bash
 # Check logs for secret loading
-gcloud app logs read --limit=100 | grep -i "secret"
+gcloud run services logs read github-copier --limit=100
 ```
 
 **Should NOT see:**
@@ -832,23 +805,23 @@ gcloud app logs read --limit=100 | grep -i "secret"
 
 ```bash
 # Watch logs during webhook delivery
-gcloud app logs tail -s default
+gcloud run services logs read github-copier --limit=50
 ```
 
 **Look for:**
-- ✅ "webhook received"
-- ✅ "signature verified"
-- ✅ "processing webhook"
+- "webhook received"
+- "signature verified"
+- "processing webhook"
 
 **Should NOT see:**
-- ❌ "webhook signature verification failed"
-- ❌ "invalid signature"
+- "webhook signature verification failed"
+- "invalid signature"
 
 ### ☐ 17. Verify File Copying
 
 ```bash
 # Watch logs during PR merge
-gcloud app logs tail -s default
+gcloud run services logs read github-copier --limit=50
 ```
 
 **Look for:**
@@ -870,7 +843,7 @@ db.audit_events.find().sort({timestamp: -1}).limit(5)
 
 ```bash
 # Check metrics endpoint
-curl https://YOUR_APP.appspot.com/metrics
+curl https://YOUR_SERVICE_URL/metrics
 ```
 
 **Expected response:**
@@ -901,9 +874,9 @@ git status | grep env.yaml
 # Should show: nothing to commit (or untracked)
 
 # Verify IAM permissions
-gcloud secrets get-iam-policy CODE_COPIER_PEM | grep @appspot
-gcloud secrets get-iam-policy webhook-secret | grep @appspot
-# Should see the service account
+gcloud secrets get-iam-policy CODE_COPIER_PEM | grep compute
+gcloud secrets get-iam-policy webhook-secret | grep compute
+# Should see the Cloud Run service account
 ```
 
 ---
@@ -939,13 +912,13 @@ gcloud secrets versions access latest --secret=webhook-secret
 **Fix:**
 ```bash
 # Option 1: Disable audit logging
-# In env.yaml: AUDIT_ENABLED: "false"
+# In env-cloudrun.yaml: AUDIT_ENABLED: "false"
 
 # Option 2: Ensure MONGO_URI_SECRET_NAME is set
-# In env.yaml: MONGO_URI_SECRET_NAME: "projects/.../secrets/mongo-uri/versions/latest"
+# In env-cloudrun.yaml: MONGO_URI_SECRET_NAME: "projects/.../secrets/mongo-uri/versions/latest"
 
 # Redeploy
-gcloud app deploy app.yaml
+./scripts/deploy-cloudrun.sh
 ```
 
 ### Error: "Config file not found"
@@ -996,20 +969,23 @@ Your application is deployed with:
 
 ---
 
-## 📚 Quick Reference
+## Quick Reference
 
 ```bash
 # Deploy
-gcloud app deploy app.yaml
+./scripts/deploy-cloudrun.sh
 
 # View logs
-gcloud app logs tail -s default
+gcloud run services logs read github-copier --limit=100
 
 # Check health
-curl https://YOUR_APP.appspot.com/health
+curl https://YOUR_SERVICE_URL/health
+
+# Check readiness
+curl https://YOUR_SERVICE_URL/ready
 
 # Check metrics
-curl https://YOUR_APP.appspot.com/metrics
+curl https://YOUR_SERVICE_URL/metrics
 
 # List secrets
 gcloud secrets list
@@ -1019,10 +995,6 @@ gcloud secrets versions access latest --secret=SECRET_NAME
 
 # Grant access
 ./scripts/grant-secret-access.sh
-
-# Rollback
-gcloud app versions list
-gcloud app services set-traffic default --splits=PREVIOUS_VERSION=1
 ```
 ---
 
@@ -1047,10 +1019,10 @@ gcloud app services set-traffic default --splits=PREVIOUS_VERSION=1
 gcloud secrets versions access latest --secret=webhook-secret
 
 # Disable audit logging
-# In env.yaml: AUDIT_ENABLED: "false"
+# In env-cloudrun.yaml: AUDIT_ENABLED: "false"
 
 # Redeploy
-gcloud app deploy app.yaml
+./scripts/deploy-cloudrun.sh
 ```
 
 ## Next Steps
diff --git a/docs/DEPRECATION-TRACKING-EXPLAINED.md b/docs/DEPRECATION-TRACKING-EXPLAINED.md
index a5947f8..3a550a8 100644
--- a/docs/DEPRECATION-TRACKING-EXPLAINED.md
+++ b/docs/DEPRECATION-TRACKING-EXPLAINED.md
@@ -320,7 +320,6 @@ Potential improvements:
 ---
 
 **See Also:**
-- [Configuration Guide](CONFIGURATION-GUIDE.md) - Deprecation configuration
 - [Architecture](ARCHITECTURE.md) - System design
 - [Troubleshooting](TROUBLESHOOTING.md) - Common issues
 
diff --git a/docs/FAQ.md b/docs/FAQ.md
index 2b8a479..a9090dd 100644
--- a/docs/FAQ.md
+++ b/docs/FAQ.md
@@ -168,7 +168,7 @@ path_transform: "all-examples/${filename}"
 
 ### What are the prerequisites?
 
-- Go 1.23.4+
+- Go 1.26+
 - GitHub App credentials
 - Google Cloud project (for Secret Manager and logging)
 - MongoDB Atlas (optional, for audit logging)
@@ -179,7 +179,7 @@ Yes! See [Local Testing](LOCAL-TESTING.md) for instructions.
 
 ### How do I deploy to Google Cloud?
 
-See [Deployment Guide](DEPLOYMENT.md) for complete guide and [Deployment Checklist](DEPLOYMENT-CHECKLIST.md) for step-by-step instructions.
+See [Deployment Guide](DEPLOYMENT.md) for the complete guide including the deployment checklist.
 
 ### Do I need MongoDB?
 
diff --git a/docs/LOCAL-TESTING.md b/docs/LOCAL-TESTING.md
index 0c4ee64..efef6a4 100644
--- a/docs/LOCAL-TESTING.md
+++ b/docs/LOCAL-TESTING.md
@@ -40,28 +40,58 @@ cp configs/.env.local.example configs/.env
 nano configs/.env
 ```
 
-### 2. Minimal Configuration
+### 2. GitHub App Credentials (Required)
 
-For basic local testing, you only need:
+The app authenticates with GitHub on startup, even in dry-run mode. You need your App ID, Installation ID, and PEM key.
+
+**Option A — PEM from GCP Secret Manager** (if you have `gcloud` access):
+
+```bash
+# Run once to authenticate locally:
+gcloud auth application-default login
+
+# configs/.env
+GITHUB_APP_ID=123456
+INSTALLATION_ID=789012
+GOOGLE_CLOUD_PROJECT_ID=github-copy-code-examples
+PEM_NAME=CODE_COPIER_PEM
+```
+
+**Option B — PEM key provided directly** (no GCP needed):
 
 ```bash
 # configs/.env
+GITHUB_APP_ID=123456
+INSTALLATION_ID=789012
+SKIP_SECRET_MANAGER=true
+GITHUB_APP_PRIVATE_KEY_B64=$(base64 -i /path/to/your-key.pem)
+```
+
+You can verify your PEM key independently with:
+
+```bash
+go build -o test-pem ./cmd/test-pem
+./test-pem /path/to/your-key.pem 123456
+```
+
+### 3. Additional Settings (Recommended)
+
+```bash
+# configs/.env (add below the credentials)
 COPIER_DISABLE_CLOUD_LOGGING=true
 DRY_RUN=true
 MAIN_CONFIG_FILE=.copier/workflows/main.yaml
 USE_MAIN_CONFIG=true
 ```
 
-### 3. For Testing with Real PRs
+### 4. For Testing with Real PRs
 
-Add a GitHub token:
+The `test-webhook` CLI and `test-with-pr.sh` script use a GitHub PAT (not the App credentials) to fetch PR data from the API:
 
 ```bash
 # Get token from: https://github.com/settings/tokens
 # Required scope: repo (read access)
-
-# Add to configs/.env
-GITHUB_TOKEN=ghp_your_token_here
+export GITHUB_TOKEN=ghp_your_token_here
 ```
 
 ## Running Locally
@@ -149,7 +179,7 @@ export WEBHOOK_SECRET=$(gcloud secrets versions access latest --secret=webhook-s
 nano .copier/workflows/main.yaml
 
 # 2. Validate it
-./config-validator validate -config config.json -v
+./config-validator validate -config copier-config.yaml -v
 
 # 3. Start app
 make run-local
@@ -207,13 +237,11 @@ Logs go to stdout when cloud logging is disabled:
 
 ```bash
 # You'll see logs like:
-[INFO] Webhook received: pull_request event
-[INFO] PR #42 merged: "Add Go database examples"
-[INFO] Processing 5 files from PR
-[DEBUG] Testing pattern: ^examples/(?P<lang>[^/]+)/(?P<category>[^/]+)/.*$
-[INFO] Pattern matched: examples/go/database/connect.go
-[INFO]   → Transformed to: docs/go/database/connect.go
-[INFO]   → Variables: lang=go, category=database
+{"level":"INFO","msg":"Webhook received","event":"pull_request"}
+{"level":"INFO","msg":"PR merged","pr":42,"title":"Add Go database examples"}
+{"level":"INFO","msg":"Processing files from PR","count":5}
+{"level":"DEBUG","msg":"Testing pattern","pattern":"^examples/(?P<lang>[^/]+)/(?P<category>[^/]+)/.*$"}
+{"level":"INFO","msg":"Pattern matched","file":"examples/go/database/connect.go","target":"docs/go/database/connect.go"}
 [DRY-RUN] Would create commit with 2 files
 [DRY-RUN] Would create PR: "Update database examples"
 ```
@@ -266,9 +294,22 @@ curl http://localhost:8080/health | jq
 
 ## Environment Variables for Local Testing
 
-### Required (Minimal)
+### Required
 
 ```bash
+# GitHub App credentials (app authenticates on startup)
+GITHUB_APP_ID=123456
+INSTALLATION_ID=789012
+
+# PEM key — Option A: via Secret Manager (requires gcloud auth)
+GOOGLE_CLOUD_PROJECT_ID=github-copy-code-examples
+PEM_NAME=CODE_COPIER_PEM
+
+# PEM key — Option B: direct (no GCP needed)
+SKIP_SECRET_MANAGER=true
+GITHUB_APP_PRIVATE_KEY_B64=<base64-encoded PEM>
+
+# Local dev overrides
 COPIER_DISABLE_CLOUD_LOGGING=true  # Use stdout instead of GCP
 DRY_RUN=true                       # Don't make actual commits
 ```
@@ -283,10 +324,10 @@ MAIN_CONFIG_FILE=.copier/workflows/main.yaml  # Your main config file
 USE_MAIN_CONFIG=true               # Enable main config system
 ```
 
-### Optional (for Real PR Testing)
+### Optional (for test-webhook CLI / test-with-pr.sh)
 
 ```bash
-GITHUB_TOKEN=ghp_...               # For fetching real PRs
+GITHUB_TOKEN=ghp_...               # PAT for fetching real PR data
 REPO_OWNER=mongodb                 # Default repo owner
 REPO_NAME=docs-realm               # Default repo name
 ```
@@ -304,9 +345,26 @@ AUDIT_COLLECTION=audit_events
 
 ## Troubleshooting
 
+### Error: "A JSON web token could not be decoded" / "Failed to configure GitHub permissions"
+
+**Problem:** The app needs GitHub App credentials (App ID + PEM key) to authenticate on startup, even in dry-run mode.
+
+**Solution:**
+```bash
+# Add to configs/.env:
+GITHUB_APP_ID=123456
+INSTALLATION_ID=789012
+
+# Then provide the PEM key — either via Secret Manager:
+gcloud auth application-default login
+# Or directly:
+SKIP_SECRET_MANAGER=true
+GITHUB_APP_PRIVATE_KEY_B64=$(base64 -i /path/to/your-key.pem)
+```
+
 ### Error: "projects/GOOGLE_CLOUD_PROJECT_ID is not a valid resource name"
 
-**Problem:** Cloud logging is enabled but GCP_PROJECT_ID is not set
+**Problem:** Cloud logging is enabled but GCP_PROJECT_ID is not set.
 
 **Solution:**
 ```bash
@@ -360,7 +418,7 @@ export GITHUB_TOKEN=ghp_your_token_here
   -file "examples/go/main.go"
 
 # Check config file
-./config-validator validate -config config.json -v
+./config-validator validate -config copier-config.yaml -v
 ```
 
 ## Complete Testing Workflow
@@ -372,7 +430,7 @@ export GITHUB_TOKEN=ghp_your_token_here
 make build
 
 # 2. Validate configuration
-./config-validator validate -config config.json -v
+./config-validator validate -config copier-config.yaml -v
 
 # 3. Test pattern matching
 ./config-validator test-pattern \
diff --git a/docs/PATTERN-MATCHING-GUIDE.md b/docs/PATTERN-MATCHING-GUIDE.md
index 59bf661..e324e71 100644
--- a/docs/PATTERN-MATCHING-GUIDE.md
+++ b/docs/PATTERN-MATCHING-GUIDE.md
@@ -846,6 +846,6 @@ ${name}      # Name without ext: main
 ## See Also
 
 - [Local Testing](LOCAL-TESTING.md) - How to test locally
-- [Quick Reference](QUICK-REFERENCE.md) - Quick command reference
+- [FAQ](FAQ.md) - Frequently asked questions
 - [Webhook Testing](WEBHOOK-TESTING.md) - Testing with webhooks
 
diff --git a/docs/TROUBLESHOOTING.md b/docs/TROUBLESHOOTING.md
index f2cc55d..8563f74 100644
--- a/docs/TROUBLESHOOTING.md
+++ b/docs/TROUBLESHOOTING.md
@@ -88,8 +88,8 @@ source configs/.env
 
 1. **Check actual file paths:**
    ```bash
-   # Look for "sample file path" in logs
-   grep "sample file path" logs/app.log
+   # Look for "sample file path" in logs (stdout or Cloud Logging)
+   # Locally: check terminal output or redirect stdout to a file
    ```
 
 2. **Test your pattern:**
@@ -206,11 +206,11 @@ pattern: "^examples/(?P<lang>[^/]+)/(?P<file>.+)$"
 
 1. **Check application logs:**
    ```bash
-   # Local
-   tail -f logs/app.log
+   # Local: logs go to stdout (JSON format)
+   LOG_LEVEL=debug ./github-copier
    
-   # GCP
-   gcloud app logs tail -s default
+   # Cloud Run
+   gcloud run services logs read github-copier --limit=50
    ```
 
 2. **Check for common errors:**
@@ -333,10 +333,7 @@ export COPIER_DISABLE_CLOUD_LOGGING=true
    # Should be: true
    ```
 
-4. **Check application logs:**
-   ```bash
-   grep "slack" logs/app.log
-   ```
+4. **Check application logs** (search stdout for "slack" in local output)
 
 ### Slack Notifications in Wrong Channel
 
@@ -469,10 +466,7 @@ db.audit_events.find().sort({timestamp: -1}).limit(10).pretty()
 
 ### Trace a Specific Request
 
-```bash
-# Look for request ID in logs
-grep "request_id=abc123" logs/app.log
-```
+Logs are structured JSON (via `log/slog`) and written to stdout. In production on Cloud Run, use Cloud Logging to search by structured fields.
 
 ## Getting Help
 
diff --git a/docs/WEBHOOK-TESTING.md b/docs/WEBHOOK-TESTING.md
index 5042e90..827db1f 100644
--- a/docs/WEBHOOK-TESTING.md
+++ b/docs/WEBHOOK-TESTING.md
@@ -87,7 +87,7 @@ Test against your staging environment:
 
 ```bash
 # Set staging URL
-export WEBHOOK_URL=https://staging-myapp.appspot.com/webhook
+export WEBHOOK_URL=https://your-service-url.run.app/events
 export WEBHOOK_SECRET=your-staging-secret
 
 # Test with real PR
@@ -172,7 +172,7 @@ EOF
 -pr int         # PR number to fetch from GitHub
 -owner string   # Repository owner (required with -pr)
 -repo string    # Repository name (required with -pr)
--url string     # Webhook URL (default: http://localhost:8080/webhook)
+-url string     # Webhook URL (default: http://localhost:8080/events)
 -secret string  # Webhook secret for HMAC signature
 -payload string # Path to custom payload JSON file
 -dry-run        # Print payload without sending
@@ -278,11 +278,11 @@ After sending a test webhook, verify:
 
 ### Application Logs
 ```bash
-# Local
-tail -f logs/app.log
+# Local: logs are JSON on stdout
+LOG_LEVEL=debug ./github-copier
 
-# GCP
-gcloud app logs tail -s default
+# Cloud Run
+gcloud run services logs read github-copier --limit=50
 ```
 
 **Look for:**
@@ -382,7 +382,7 @@ db.audit_events.find().sort({timestamp: -1}).limit(10)
 curl http://localhost:8080/health
 
 # Check webhook URL
-./test-webhook -payload test.json -url http://localhost:8080/webhook
+./test-webhook -payload test.json -url http://localhost:8080/events
 
 # Check application logs for errors
 ```
diff --git a/env-cloudrun.yaml b/env-cloudrun.yaml
index a255f63..48fe1fd 100644
--- a/env-cloudrun.yaml
+++ b/env-cloudrun.yaml
@@ -2,19 +2,19 @@
 # Format: KEY: "VALUE" (no env_variables wrapper needed)
 # Note: PORT is automatically set by Cloud Run, don't override it
 
-# GitHub Configuration
-GITHUB_APP_ID: "1166559"
-INSTALLATION_ID: "95537167" # grove-platform
+# Org-specific values (GITHUB_APP_ID, INSTALLATION_ID) are passed via
+# --set-env-vars in the deploy step using GitHub Actions secrets.
+# Do NOT commit org-specific values here.
 
 # Config Repository (where main config file is stored)
 CONFIG_REPO_OWNER: "grove-platform"
 CONFIG_REPO_NAME: "github-copier"
 CONFIG_REPO_BRANCH: "main"
 
-# Secret Manager References
-GITHUB_APP_PRIVATE_KEY_SECRET_NAME: "projects/1054147886816/secrets/CODE_COPIER_PEM/versions/latest"
-WEBHOOK_SECRET_NAME: "projects/1054147886816/secrets/webhook-secret/versions/latest"
-MONGO_URI_SECRET_NAME: "projects/1054147886816/secrets/mongo-uri/versions/latest"
+# Secret Manager References (short names — resolved at runtime via SecretPath())
+PEM_NAME: "CODE_COPIER_PEM"
+WEBHOOK_SECRET_NAME: "webhook-secret"
+MONGO_URI_SECRET_NAME: "mongo-uri"
 
 # Application Settings
 WEBSERVER_PATH: "/events"
@@ -33,4 +33,3 @@ COPIER_LOG_NAME: "code-copier-log"
 # Feature Flags
 AUDIT_ENABLED: "false"
 METRICS_ENABLED: "true"
-
diff --git a/github-app-manifest.yml b/github-app-manifest.yml
new file mode 100644
index 0000000..3e00db1
--- /dev/null
+++ b/github-app-manifest.yml
@@ -0,0 +1,46 @@
+# GitHub App Manifest
+# Documents the minimum permissions and events required by this GitHub App.
+# Reference: https://docs.github.com/en/apps/sharing-github-apps/registering-a-github-app-from-a-manifest
+#
+# This file serves as living documentation. It can also be used with GitHub's
+# "Register a GitHub App from a manifest" flow to create a correctly configured app.
+
+name: GitHub Copier
+description: Copies code examples between repositories when pull requests are merged.
+url: https://github.com/grove-platform/github-copier
+
+# --- Permissions ---
+# The minimum set of permissions needed for the app to function.
+
+default_permissions:
+  # Read & Write: read source files, create branches/trees/commits, push to target repos,
+  # read config repos, update deprecation files.
+  contents: write
+
+  # Read & Write: read changed files via GraphQL, create PRs in target repos,
+  # check mergeability, auto-merge PRs.
+  pull_requests: write
+
+  # Read: implicit for all GitHub Apps; required for basic repository access.
+  metadata: read
+
+# --- Webhook Events ---
+# The app only needs the pull_request event. It processes merged PRs
+# (action == "closed" && merged == true) and ignores all other events.
+
+default_events:
+  - pull_request
+
+# --- Installation ---
+# The app must be installed in every organization whose repositories it accesses:
+#   - Source repos (where PRs trigger the webhook)
+#   - Target repos (where files are copied to)
+#   - Config repo  (where workflow YAML files live)
+#
+# The app discovers per-org installation IDs at runtime via GET /app/installations
+# and creates scoped installation access tokens for each org.
+
+# --- Webhook Configuration ---
+# The app listens on /events for webhook deliveries.
+# Configure the webhook URL to point to your Cloud Run service URL + /events.
+# A webhook secret (WEBHOOK_SECRET) should always be configured in production.
diff --git a/go.mod b/go.mod
index 3a6d555..bec8756 100644
--- a/go.mod
+++ b/go.mod
@@ -1,63 +1,62 @@
 module github.com/grove-platform/github-copier
 
-go 1.24.0
+go 1.26.0
 
 require (
-	cloud.google.com/go/logging v1.13.0
-	cloud.google.com/go/secretmanager v1.14.6
-	github.com/bmatcuk/doublestar/v4 v4.9.1
-	github.com/golang-jwt/jwt/v5 v5.2.2
-	github.com/google/go-github/v48 v48.2.0
-	github.com/jarcoal/httpmock v1.4.0
+	cloud.google.com/go/logging v1.13.2
+	cloud.google.com/go/secretmanager v1.16.0
+	github.com/bmatcuk/doublestar/v4 v4.10.0
+	github.com/golang-jwt/jwt/v5 v5.3.1
+	github.com/google/go-github/v82 v82.0.0
+	github.com/google/uuid v1.6.0
+	github.com/jarcoal/httpmock v1.4.1
 	github.com/joho/godotenv v1.5.1
-	github.com/pkg/errors v0.9.1
-	github.com/shurcooL/githubv4 v0.0.0-20240727222349-48295856cce7
-	github.com/shurcooL/graphql v0.0.0-20230722043721-ed46e5a46466
-	github.com/stretchr/testify v1.10.0
-	go.mongodb.org/mongo-driver v1.17.1
-	golang.org/x/oauth2 v0.28.0
+	github.com/shurcooL/githubv4 v0.0.0-20260209031235-2402fdf4a9ed
+	github.com/shurcooL/graphql v0.0.0-20240915155400-7ee5256398cf
+	github.com/stretchr/testify v1.11.1
+	go.mongodb.org/mongo-driver/v2 v2.5.0
+	golang.org/x/oauth2 v0.35.0
 	gopkg.in/yaml.v3 v3.0.1
 )
 
 require (
-	cloud.google.com/go v0.118.3 // indirect
-	cloud.google.com/go/auth v0.15.0 // indirect
-	cloud.google.com/go/auth/oauth2adapt v0.2.7 // indirect
-	cloud.google.com/go/compute/metadata v0.6.0 // indirect
-	cloud.google.com/go/iam v1.4.1 // indirect
-	cloud.google.com/go/longrunning v0.6.4 // indirect
+	cloud.google.com/go v0.123.0 // indirect
+	cloud.google.com/go/auth v0.18.0 // indirect
+	cloud.google.com/go/auth/oauth2adapt v0.2.8 // indirect
+	cloud.google.com/go/compute/metadata v0.9.0 // indirect
+	cloud.google.com/go/iam v1.5.3 // indirect
+	cloud.google.com/go/longrunning v0.8.0 // indirect
+	github.com/cespare/xxhash/v2 v2.3.0 // indirect
 	github.com/davecgh/go-spew v1.1.1 // indirect
 	github.com/felixge/httpsnoop v1.0.4 // indirect
-	github.com/go-logr/logr v1.4.2 // indirect
+	github.com/go-logr/logr v1.4.3 // indirect
 	github.com/go-logr/stdr v1.2.2 // indirect
-	github.com/golang/snappy v0.0.4 // indirect
-	github.com/google/go-querystring v1.1.0 // indirect
+	github.com/google/go-querystring v1.2.0 // indirect
 	github.com/google/s2a-go v0.1.9 // indirect
-	github.com/googleapis/enterprise-certificate-proxy v0.3.5 // indirect
-	github.com/googleapis/gax-go/v2 v2.14.1 // indirect
-	github.com/klauspost/compress v1.13.6 // indirect
-	github.com/montanaflynn/stats v0.7.1 // indirect
+	github.com/googleapis/enterprise-certificate-proxy v0.3.7 // indirect
+	github.com/googleapis/gax-go/v2 v2.16.0 // indirect
+	github.com/klauspost/compress v1.17.6 // indirect
 	github.com/pmezard/go-difflib v1.0.0 // indirect
 	github.com/xdg-go/pbkdf2 v1.0.0 // indirect
-	github.com/xdg-go/scram v1.1.2 // indirect
+	github.com/xdg-go/scram v1.2.0 // indirect
 	github.com/xdg-go/stringprep v1.0.4 // indirect
 	github.com/youmark/pkcs8 v0.0.0-20240726163527-a2c0da244d78 // indirect
-	go.opentelemetry.io/auto/sdk v1.1.0 // indirect
-	go.opentelemetry.io/contrib/instrumentation/google.golang.org/grpc/otelgrpc v0.59.0 // indirect
-	go.opentelemetry.io/contrib/instrumentation/net/http/otelhttp v0.59.0 // indirect
-	go.opentelemetry.io/otel v1.34.0 // indirect
-	go.opentelemetry.io/otel/metric v1.34.0 // indirect
-	go.opentelemetry.io/otel/trace v1.34.0 // indirect
-	golang.org/x/crypto v0.45.0 // indirect
-	golang.org/x/net v0.47.0 // indirect
-	golang.org/x/sync v0.18.0 // indirect
-	golang.org/x/sys v0.38.0 // indirect
-	golang.org/x/text v0.31.0 // indirect
-	golang.org/x/time v0.10.0 // indirect
-	google.golang.org/api v0.224.0 // indirect
-	google.golang.org/genproto v0.0.0-20250303144028-a0af3efb3deb // indirect
-	google.golang.org/genproto/googleapis/api v0.0.0-20250303144028-a0af3efb3deb // indirect
-	google.golang.org/genproto/googleapis/rpc v0.0.0-20250227231956-55c901821b1e // indirect
-	google.golang.org/grpc v1.71.0 // indirect
-	google.golang.org/protobuf v1.36.5 // indirect
+	go.opentelemetry.io/auto/sdk v1.2.1 // indirect
+	go.opentelemetry.io/contrib/instrumentation/google.golang.org/grpc/otelgrpc v0.63.0 // indirect
+	go.opentelemetry.io/contrib/instrumentation/net/http/otelhttp v0.61.0 // indirect
+	go.opentelemetry.io/otel v1.39.0 // indirect
+	go.opentelemetry.io/otel/metric v1.39.0 // indirect
+	go.opentelemetry.io/otel/trace v1.39.0 // indirect
+	golang.org/x/crypto v0.46.0 // indirect
+	golang.org/x/net v0.48.0 // indirect
+	golang.org/x/sync v0.19.0 // indirect
+	golang.org/x/sys v0.39.0 // indirect
+	golang.org/x/text v0.32.0 // indirect
+	golang.org/x/time v0.14.0 // indirect
+	google.golang.org/api v0.259.0 // indirect
+	google.golang.org/genproto v0.0.0-20251202230838-ff82c1b0f217 // indirect
+	google.golang.org/genproto/googleapis/api v0.0.0-20251222181119-0a764e51fe1b // indirect
+	google.golang.org/genproto/googleapis/rpc v0.0.0-20251222181119-0a764e51fe1b // indirect
+	google.golang.org/grpc v1.78.0 // indirect
+	google.golang.org/protobuf v1.36.11 // indirect
 )
diff --git a/go.sum b/go.sum
index 2e3e5ab..ca3e2ee 100644
--- a/go.sum
+++ b/go.sum
@@ -1,158 +1,164 @@
-cloud.google.com/go v0.118.3 h1:jsypSnrE/w4mJysioGdMBg4MiW/hHx/sArFpaBWHdME=
-cloud.google.com/go v0.118.3/go.mod h1:Lhs3YLnBlwJ4KA6nuObNMZ/fCbOQBPuWKPoE0Wa/9Vc=
-cloud.google.com/go/auth v0.15.0 h1:Ly0u4aA5vG/fsSsxu98qCQBemXtAtJf+95z9HK+cxps=
-cloud.google.com/go/auth v0.15.0/go.mod h1:WJDGqZ1o9E9wKIL+IwStfyn/+s59zl4Bi+1KQNVXLZ8=
-cloud.google.com/go/auth/oauth2adapt v0.2.7 h1:/Lc7xODdqcEw8IrZ9SvwnlLX6j9FHQM74z6cBk9Rw6M=
-cloud.google.com/go/auth/oauth2adapt v0.2.7/go.mod h1:NTbTTzfvPl1Y3V1nPpOgl2w6d/FjO7NNUQaWSox6ZMc=
-cloud.google.com/go/compute/metadata v0.6.0 h1:A6hENjEsCDtC1k8byVsgwvVcioamEHvZ4j01OwKxG9I=
-cloud.google.com/go/compute/metadata v0.6.0/go.mod h1:FjyFAW1MW0C203CEOMDTu3Dk1FlqW3Rga40jzHL4hfg=
-cloud.google.com/go/iam v1.4.1 h1:cFC25Nv+u5BkTR/BT1tXdoF2daiVbZ1RLx2eqfQ9RMM=
-cloud.google.com/go/iam v1.4.1/go.mod h1:2vUEJpUG3Q9p2UdsyksaKpDzlwOrnMzS30isdReIcLM=
-cloud.google.com/go/logging v1.13.0 h1:7j0HgAp0B94o1YRDqiqm26w4q1rDMH7XNRU34lJXHYc=
-cloud.google.com/go/logging v1.13.0/go.mod h1:36CoKh6KA/M0PbhPKMq6/qety2DCAErbhXT62TuXALA=
-cloud.google.com/go/longrunning v0.6.4 h1:3tyw9rO3E2XVXzSApn1gyEEnH2K9SynNQjMlBi3uHLg=
-cloud.google.com/go/longrunning v0.6.4/go.mod h1:ttZpLCe6e7EXvn9OxpBRx7kZEB0efv8yBO6YnVMfhJs=
-cloud.google.com/go/secretmanager v1.14.6 h1:/ooktIMSORaWk9gm3vf8+Mg+zSrUplJFKBztP993oL0=
-cloud.google.com/go/secretmanager v1.14.6/go.mod h1:0OWeM3qpJ2n71MGgNfKsgjC/9LfVTcUqXFUlGxo5PzY=
-github.com/bmatcuk/doublestar/v4 v4.9.1 h1:X8jg9rRZmJd4yRy7ZeNDRnM+T3ZfHv15JiBJ/avrEXE=
-github.com/bmatcuk/doublestar/v4 v4.9.1/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
+cloud.google.com/go v0.123.0 h1:2NAUJwPR47q+E35uaJeYoNhuNEM9kM8SjgRgdeOJUSE=
+cloud.google.com/go v0.123.0/go.mod h1:xBoMV08QcqUGuPW65Qfm1o9Y4zKZBpGS+7bImXLTAZU=
+cloud.google.com/go/auth v0.18.0 h1:wnqy5hrv7p3k7cShwAU/Br3nzod7fxoqG+k0VZ+/Pk0=
+cloud.google.com/go/auth v0.18.0/go.mod h1:wwkPM1AgE1f2u6dG443MiWoD8C3BtOywNsUMcUTVDRo=
+cloud.google.com/go/auth/oauth2adapt v0.2.8 h1:keo8NaayQZ6wimpNSmW5OPc283g65QNIiLpZnkHRbnc=
+cloud.google.com/go/auth/oauth2adapt v0.2.8/go.mod h1:XQ9y31RkqZCcwJWNSx2Xvric3RrU88hAYYbjDWYDL+c=
+cloud.google.com/go/compute/metadata v0.9.0 h1:pDUj4QMoPejqq20dK0Pg2N4yG9zIkYGdBtwLoEkH9Zs=
+cloud.google.com/go/compute/metadata v0.9.0/go.mod h1:E0bWwX5wTnLPedCKqk3pJmVgCBSM6qQI1yTBdEb3C10=
+cloud.google.com/go/iam v1.5.3 h1:+vMINPiDF2ognBJ97ABAYYwRgsaqxPbQDlMnbHMjolc=
+cloud.google.com/go/iam v1.5.3/go.mod h1:MR3v9oLkZCTlaqljW6Eb2d3HGDGK5/bDv93jhfISFvU=
+cloud.google.com/go/logging v1.13.2 h1:qqlHCBvieJT9Cdq4QqYx1KPadCQ2noD4FK02eNqHAjA=
+cloud.google.com/go/logging v1.13.2/go.mod h1:zaybliM3yun1J8mU2dVQ1/qDzjbOqEijZCn6hSBtKak=
+cloud.google.com/go/longrunning v0.8.0 h1:LiKK77J3bx5gDLi4SMViHixjD2ohlkwBi+mKA7EhfW8=
+cloud.google.com/go/longrunning v0.8.0/go.mod h1:UmErU2Onzi+fKDg2gR7dusz11Pe26aknR4kHmJJqIfk=
+cloud.google.com/go/secretmanager v1.16.0 h1:19QT7ZsLJ8FSP1k+4esQvuCD7npMJml6hYzilxVyT+k=
+cloud.google.com/go/secretmanager v1.16.0/go.mod h1://C/e4I8D26SDTz1f3TQcddhcmiC3rMEl0S1Cakvs3Q=
+github.com/bmatcuk/doublestar/v4 v4.10.0 h1:zU9WiOla1YA122oLM6i4EXvGW62DvKZVxIe6TYWexEs=
+github.com/bmatcuk/doublestar/v4 v4.10.0/go.mod h1:xBQ8jztBU6kakFMg+8WGxn0c6z1fTSPVIjEY1Wr7jzc=
+github.com/cespare/xxhash/v2 v2.3.0 h1:UL815xU9SqsFlibzuggzjXhog7bL6oX9BbNZnL2UFvs=
+github.com/cespare/xxhash/v2 v2.3.0/go.mod h1:VGX0DQ3Q6kWi7AoAeZDth3/j3BFtOZR5XLFGgcrjCOs=
+github.com/cncf/xds/go v0.0.0-20251022180443-0feb69152e9f h1:Y8xYupdHxryycyPlc9Y+bSQAYZnetRJ70VMVKm5CKI0=
+github.com/cncf/xds/go v0.0.0-20251022180443-0feb69152e9f/go.mod h1:HlzOvOjVBOfTGSRXRyY0OiCS/3J1akRGQQpRO/7zyF4=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
+github.com/envoyproxy/go-control-plane v0.13.5-0.20251024222203-75eaa193e329 h1:K+fnvUM0VZ7ZFJf0n4L/BRlnsb9pL/GuDG6FqaH+PwM=
+github.com/envoyproxy/go-control-plane/envoy v1.35.0 h1:ixjkELDE+ru6idPxcHLj8LBVc2bFP7iBytj353BoHUo=
+github.com/envoyproxy/go-control-plane/envoy v1.35.0/go.mod h1:09qwbGVuSWWAyN5t/b3iyVfz5+z8QWGrzkoqm/8SbEs=
+github.com/envoyproxy/protoc-gen-validate v1.2.1 h1:DEo3O99U8j4hBFwbJfrz9VtgcDfUKS7KJ7spH3d86P8=
+github.com/envoyproxy/protoc-gen-validate v1.2.1/go.mod h1:d/C80l/jxXLdfEIhX1W2TmLfsJ31lvEjwamM4DxlWXU=
 github.com/felixge/httpsnoop v1.0.4 h1:NFTV2Zj1bL4mc9sqWACXbQFVBBg2W3GPvqp8/ESS2Wg=
 github.com/felixge/httpsnoop v1.0.4/go.mod h1:m8KPJKqk1gH5J9DgRY2ASl2lWCfGKXixSwevea8zH2U=
 github.com/go-logr/logr v1.2.2/go.mod h1:jdQByPbusPIv2/zmleS9BjJVeZ6kBagPoEUsqbVz/1A=
-github.com/go-logr/logr v1.4.2 h1:6pFjapn8bFcIbiKo3XT4j/BhANplGihG6tvd+8rYgrY=
-github.com/go-logr/logr v1.4.2/go.mod h1:9T104GzyrTigFIr8wt5mBrctHMim0Nb2HLGrmQ40KvY=
+github.com/go-logr/logr v1.4.3 h1:CjnDlHq8ikf6E492q6eKboGOC0T8CDaOvkHCIg8idEI=
+github.com/go-logr/logr v1.4.3/go.mod h1:9T104GzyrTigFIr8wt5mBrctHMim0Nb2HLGrmQ40KvY=
 github.com/go-logr/stdr v1.2.2 h1:hSWxHoqTgW2S2qGc0LTAI563KZ5YKYRhT3MFKZMbjag=
 github.com/go-logr/stdr v1.2.2/go.mod h1:mMo/vtBO5dYbehREoey6XUKy/eSumjCCveDpRre4VKE=
-github.com/golang-jwt/jwt/v5 v5.2.2 h1:Rl4B7itRWVtYIHFrSNd7vhTiz9UpLdi6gZhZ3wEeDy8=
-github.com/golang-jwt/jwt/v5 v5.2.2/go.mod h1:pqrtFR0X4osieyHYxtmOUWsAWrfe1Q5UVIyoH402zdk=
+github.com/golang-jwt/jwt/v5 v5.3.1 h1:kYf81DTWFe7t+1VvL7eS+jKFVWaUnK9cB1qbwn63YCY=
+github.com/golang-jwt/jwt/v5 v5.3.1/go.mod h1:fxCRLWMO43lRc8nhHWY6LGqRcf+1gQWArsqaEUEa5bE=
 github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da h1:oI5xCqsCo564l8iNU+DwB5epxmsaqB+rhGL0m5jtYqE=
 github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc=
 github.com/golang/protobuf v1.5.4 h1:i7eJL8qZTpSEXOPTxNKhASYpMn+8e5Q6AdndVa1dWek=
 github.com/golang/protobuf v1.5.4/go.mod h1:lnTiLA8Wa4RWRcIUkrtSVa5nRhsEGBg48fD6rSs7xps=
-github.com/golang/snappy v0.0.4 h1:yAGX7huGHXlcLOEtBnF4w7FQwA26wojNCwOYAEhLjQM=
-github.com/golang/snappy v0.0.4/go.mod h1:/XxbfmMg8lxefKM7IXC3fBNl/7bRcc72aCRzEWrmP2Q=
-github.com/google/go-cmp v0.5.2/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
+github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
 github.com/google/go-cmp v0.7.0 h1:wk8382ETsv4JYUZwIsn6YpYiWiBsYLSJiTsyBybVuN8=
 github.com/google/go-cmp v0.7.0/go.mod h1:pXiqmnSA92OHEEa9HXL2W4E7lf9JzCmGVUdgjX3N/iU=
-github.com/google/go-github/v48 v48.2.0 h1:68puzySE6WqUY9KWmpOsDEQfDZsso98rT6pZcz9HqcE=
-github.com/google/go-github/v48 v48.2.0/go.mod h1:dDlehKBDo850ZPvCTK0sEqTCVWcrGl2LcDiajkYi89Y=
-github.com/google/go-querystring v1.1.0 h1:AnCroh3fv4ZBgVIf1Iwtovgjaw/GiKJo8M8yD/fhyJ8=
-github.com/google/go-querystring v1.1.0/go.mod h1:Kcdr2DB4koayq7X8pmAG4sNG59So17icRSOU623lUBU=
+github.com/google/go-github/v82 v82.0.0 h1:OH09ESON2QwKCUVMYmMcVu1IFKFoaZHwqYaUtr/MVfk=
+github.com/google/go-github/v82 v82.0.0/go.mod h1:hQ6Xo0VKfL8RZ7z1hSfB4fvISg0QqHOqe9BP0qo+WvM=
+github.com/google/go-querystring v1.2.0 h1:yhqkPbu2/OH+V9BfpCVPZkNmUXhb2gBxJArfhIxNtP0=
+github.com/google/go-querystring v1.2.0/go.mod h1:8IFJqpSRITyJ8QhQ13bmbeMBDfmeEJZD5A0egEOmkqU=
 github.com/google/s2a-go v0.1.9 h1:LGD7gtMgezd8a/Xak7mEWL0PjoTQFvpRudN895yqKW0=
 github.com/google/s2a-go v0.1.9/go.mod h1:YA0Ei2ZQL3acow2O62kdp9UlnvMmU7kA6Eutn0dXayM=
 github.com/google/uuid v1.6.0 h1:NIvaJDMOsjHA8n1jAhLSgzrAzy1Hgr+hNrb57e+94F0=
 github.com/google/uuid v1.6.0/go.mod h1:TIyPZe4MgqvfeYDBFedMoGGpEw/LqOeaOT+nhxU+yHo=
-github.com/googleapis/enterprise-certificate-proxy v0.3.5 h1:VgzTY2jogw3xt39CusEnFJWm7rlsq5yL5q9XdLOuP5g=
-github.com/googleapis/enterprise-certificate-proxy v0.3.5/go.mod h1:MkHOF77EYAE7qfSuSS9PU6g4Nt4e11cnsDUowfwewLA=
-github.com/googleapis/gax-go/v2 v2.14.1 h1:hb0FFeiPaQskmvakKu5EbCbpntQn48jyHuvrkurSS/Q=
-github.com/googleapis/gax-go/v2 v2.14.1/go.mod h1:Hb/NubMaVM88SrNkvl8X/o8XWwDJEPqouaLeN2IUxoA=
-github.com/jarcoal/httpmock v1.4.0 h1:BvhqnH0JAYbNudL2GMJKgOHe2CtKlzJ/5rWKyp+hc2k=
-github.com/jarcoal/httpmock v1.4.0/go.mod h1:ftW1xULwo+j0R0JJkJIIi7UKigZUXCLLanykgjwBXL0=
+github.com/googleapis/enterprise-certificate-proxy v0.3.7 h1:zrn2Ee/nWmHulBx5sAVrGgAa0f2/R35S4DJwfFaUPFQ=
+github.com/googleapis/enterprise-certificate-proxy v0.3.7/go.mod h1:MkHOF77EYAE7qfSuSS9PU6g4Nt4e11cnsDUowfwewLA=
+github.com/googleapis/gax-go/v2 v2.16.0 h1:iHbQmKLLZrexmb0OSsNGTeSTS0HO4YvFOG8g5E4Zd0Y=
+github.com/googleapis/gax-go/v2 v2.16.0/go.mod h1:o1vfQjjNZn4+dPnRdl/4ZD7S9414Y4xA+a/6Icj6l14=
+github.com/jarcoal/httpmock v1.4.1 h1:0Ju+VCFuARfFlhVXFc2HxlcQkfB+Xq12/EotHko+x2A=
+github.com/jarcoal/httpmock v1.4.1/go.mod h1:ftW1xULwo+j0R0JJkJIIi7UKigZUXCLLanykgjwBXL0=
 github.com/joho/godotenv v1.5.1 h1:7eLL/+HRGLY0ldzfGMeQkb7vMd0as4CfYvUVzLqw0N0=
 github.com/joho/godotenv v1.5.1/go.mod h1:f4LDr5Voq0i2e/R5DDNOoa2zzDfwtkZa6DnEwAbqwq4=
-github.com/klauspost/compress v1.13.6 h1:P76CopJELS0TiO2mebmnzgWaajssP/EszplttgQxcgc=
-github.com/klauspost/compress v1.13.6/go.mod h1:/3/Vjq9QcHkK5uEr5lBEmyoZ1iFhe47etQ6QUkpK6sk=
+github.com/klauspost/compress v1.17.6 h1:60eq2E/jlfwQXtvZEeBUYADs+BwKBWURIY+Gj2eRGjI=
+github.com/klauspost/compress v1.17.6/go.mod h1:/dCuZOvVtNoHsyb+cuJD3itjs3NbnF6KH9zAO4BDxPM=
 github.com/kr/pretty v0.3.1 h1:flRD4NNwYAUpkphVc1HcthR4KEIFJ65n8Mw5qdRn3LE=
 github.com/kr/pretty v0.3.1/go.mod h1:hoEshYVHaxMs3cyo3Yncou5ZscifuDolrwPKZanG3xk=
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-google.golang.org/genproto v0.0.0-20250303144028-a0af3efb3deb/go.mod h1:sAo5UzpjUwgFBCzupwhcLcxHVDK7vG5IqI30YnwX2eE=
-google.golang.org/genproto/googleapis/api v0.0.0-20250303144028-a0af3efb3deb h1:p31xT4yrYrSM/G4Sn2+TNUkVhFCbG9y8itM2S6Th950=
-google.golang.org/genproto/googleapis/api v0.0.0-20250303144028-a0af3efb3deb/go.mod h1:jbe3Bkdp+Dh2IrslsFCklNhweNTBgSYanP1UXhJDhKg=
-google.golang.org/genproto/googleapis/rpc v0.0.0-20250227231956-55c901821b1e h1:YA5lmSs3zc/5w+xsRcHqpETkaYyK63ivEPzNTcUUlSA=
-google.golang.org/genproto/googleapis/rpc v0.0.0-20250227231956-55c901821b1e/go.mod h1:LuRYeWDFV6WOn90g357N17oMCaxpgCnbi/44qJvDn2I=
-google.golang.org/grpc v1.71.0 h1:kF77BGdPTQ4/JZWMlb9VpJ5pa25aqvVqogsxNHHdeBg=
-google.golang.org/grpc v1.71.0/go.mod h1:H0GRtasmQOh9LkFoCPDu3ZrwUtD1YGE+b2vYBYd/8Ec=
-google.golang.org/protobuf v1.36.5 h1:tPhr+woSbjfYvY6/GPufUoYizxw1cF/yFoxJ2fmpwlM=
-google.golang.org/protobuf v1.36.5/go.mod h1:9fA7Ob0pmnwhb644+1+CVWFRbNajQ6iRojtC/QF5bRE=
+gonum.org/v1/gonum v0.16.0 h1:5+ul4Swaf3ESvrOnidPp4GZbzf0mxVQpDCYUQE7OJfk=
+gonum.org/v1/gonum v0.16.0/go.mod h1:fef3am4MQ93R2HHpKnLk4/Tbh/s0+wqD5nfa6Pnwy4E=
+google.golang.org/api v0.259.0 h1:90TaGVIxScrh1Vn/XI2426kRpBqHwWIzVBzJsVZ5XrQ=
+google.golang.org/api v0.259.0/go.mod h1:LC2ISWGWbRoyQVpxGntWwLWN/vLNxxKBK9KuJRI8Te4=
+google.golang.org/genproto v0.0.0-20251202230838-ff82c1b0f217 h1:GvESR9BIyHUahIb0NcTum6itIWtdoglGX+rnGxm2934=
+google.golang.org/genproto v0.0.0-20251202230838-ff82c1b0f217/go.mod h1:yJ2HH4EHEDTd3JiLmhds6NkJ17ITVYOdV3m3VKOnws0=
+google.golang.org/genproto/googleapis/api v0.0.0-20251222181119-0a764e51fe1b h1:uA40e2M6fYRBf0+8uN5mLlqUtV192iiksiICIBkYJ1E=
+google.golang.org/genproto/googleapis/api v0.0.0-20251222181119-0a764e51fe1b/go.mod h1:Xa7le7qx2vmqB/SzWUBa7KdMjpdpAHlh5QCSnjessQk=
+google.golang.org/genproto/googleapis/rpc v0.0.0-20251222181119-0a764e51fe1b h1:Mv8VFug0MP9e5vUxfBcE3vUkV6CImK3cMNMIDFjmzxU=
+google.golang.org/genproto/googleapis/rpc v0.0.0-20251222181119-0a764e51fe1b/go.mod h1:j9x/tPzZkyxcgEFkiKEEGxfvyumM01BEtsW8xzOahRQ=
+google.golang.org/grpc v1.78.0 h1:K1XZG/yGDJnzMdd/uZHAkVqJE+xIDOcmdSFZkBUicNc=
+google.golang.org/grpc v1.78.0/go.mod h1:I47qjTo4OKbMkjA/aOOwxDIiPSBofUtQUI5EfpWvW7U=
+google.golang.org/protobuf v1.36.11 h1:fV6ZwhNocDyBLK0dj+fg8ektcVegBBuEolpbTQyBNVE=
+google.golang.org/protobuf v1.36.11/go.mod h1:HTf+CrKn2C3g5S8VImy6tdcUvCska2kB7j23XfzDpco=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
diff --git a/scripts/README.md b/scripts/README.md
index c6a3c01..4286520 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -1,233 +1,156 @@
 # Helper Scripts
 
-Collection of helper scripts for testing and running the github-copier application.
+Collection of helper scripts for developing, testing, and deploying the github-copier application.
 
 ## Scripts
 
-### run-local.sh
+### ci-local.sh
 
-Start the github-copier application locally with proper environment configuration.
+Run the full CI pipeline locally before pushing. Mirrors what `.github/workflows/ci.yml` does.
 
 **Usage:**
 ```bash
-./scripts/run-local.sh
+./scripts/ci-local.sh
 ```
 
 **What it does:**
-- Loads environment variables from `configs/.env.local`
-- Disables Google Cloud logging (uses stdout instead)
-- Sets up local configuration
-- Starts the application
+1. `go build ./...`
+2. `go test -race ./...`
+3. `golangci-lint run ./...`
+4. `go vet ./...`
+
+### run-local.sh
+
+Start the github-copier application locally with development settings.
 
-**Example:**
+**Usage:**
 ```bash
-# Start app locally
 ./scripts/run-local.sh
-
-# In another terminal, test it
-./test-webhook -payload testdata/example-pr-merged.json
 ```
 
-**Environment:**
-- Uses `configs/.env.local` for configuration
-- Sets `COPIER_DISABLE_CLOUD_LOGGING=true`
-- Sets `CONFIG_FILE=copier-config.yaml`
+**What it does:**
+- Builds the `github-copier` binary if needed
+- Disables Google Cloud logging (uses stdout)
+- Enables dry-run mode, debug logging, and metrics
+- Loads env from `configs/.env` if present
+- Starts the application on port 8080
 
-### test-and-check.sh
+### deploy-cloudrun.sh
 
-Send a test webhook and check the metrics.
+Deploy to Google Cloud Run.
 
 **Usage:**
 ```bash
-./scripts/test-and-check.sh
+./scripts/deploy-cloudrun.sh [region]
 ```
 
 **What it does:**
-1. Sends test webhook with example payload
-2. Waits for processing
-3. Fetches and displays metrics
-4. Shows recent application logs
+- Validates `env-cloudrun.yaml` exists
+- Confirms deployment with user
+- Deploys via `gcloud run deploy` with Dockerfile
+- Prints service URL and next steps
 
-**Example:**
-```bash
-# Start app first
-./scripts/run-local.sh
+### grant-secret-access.sh
 
-# In another terminal, test and check
-./scripts/test-and-check.sh
-```
+Grant the Cloud Run service account access to all required secrets in Secret Manager.
 
-**Output:**
-```
-Testing webhook with example payload...
-
-✓ Loaded payload from testdata/example-pr-merged.json
-✓ Response: 200 OK
-✓ Webhook sent successfully
-
-Webhook sent! Waiting 2 seconds for processing...
-
-=== Metrics ===
-{
-  "webhooks": {
-    "received": 1,
-    "processed": 1,
-    "failed": 0
-  },
-  "files": {
-    "matched": 20,
-    "uploaded": 0
-  }
-}
-
-=== Recent Logs ===
-[INFO] loaded config from local file
-[INFO] retrieved changed files | {"count":21}
-[INFO] processing files with pattern matching
-[INFO] file matched pattern | {"file":"..."}
+**Usage:**
+```bash
+./scripts/grant-secret-access.sh
 ```
 
-### test-slack.sh
+**Secrets configured:** `CODE_COPIER_PEM`, `webhook-secret`, `mongo-uri`
 
-Test Slack notifications by sending example messages.
+### test-and-check.sh
+
+Send a test webhook and check health/metrics.
 
 **Usage:**
 ```bash
-./scripts/test-slack.sh [webhook-url]
+./scripts/test-and-check.sh
 ```
 
-**Arguments:**
-- `webhook-url` - Slack webhook URL (optional, uses `$SLACK_WEBHOOK_URL` if not provided)
-
 **What it does:**
-1. Sends simple test message
-2. Sends PR processed notification
-3. Sends error notification
-4. Sends files copied notification
-5. Sends deprecation notification
+1. Sends test webhook with example payload
+2. Waits for processing
+3. Fetches and displays `/metrics` and `/health`
 
-**Example:**
-```bash
-# Using environment variable
-export SLACK_WEBHOOK_URL="https://hooks.slack.com/services/..."
-./scripts/test-slack.sh
+### test-with-pr.sh
 
-# Or pass URL directly
-./scripts/test-slack.sh "https://hooks.slack.com/services/..."
-```
+Fetch real PR data from GitHub and send it to the webhook.
 
-**Output:**
+**Usage:**
+```bash
+./scripts/test-with-pr.sh <pr-number> [owner] [repo]
 ```
-Testing Slack Notifications
-
-Webhook URL: https://hooks.slack.com/services/...
-
-Test 1: Sending simple test message...
-✓ Simple message sent
-
-Test 2: Sending PR processed notification...
-✓ PR processed notification sent
-
-Test 3: Sending error notification...
-✓ Error notification sent
-
-Test 4: Sending files copied notification...
-✓ Files copied notification sent
-
-Test 5: Sending deprecation notification...
-✓ Deprecation notification sent
-
-=== All Tests Complete ===
 
-Check your Slack channel for 5 test notifications
-```
+**Environment:**
+- `GITHUB_TOKEN` — GitHub personal access token (required)
+- `WEBHOOK_URL` — Webhook endpoint (default: `http://localhost:8080/events`)
+- `WEBHOOK_SECRET` — Webhook secret for HMAC signature
 
-### convert-env-format.sh
+### integration-test.sh
 
-Convert between App Engine and Cloud Run environment file formats.
+End-to-end integration test: sends a webhook payload and optionally verifies destination repos.
 
 **Usage:**
 ```bash
-./scripts/convert-env-format.sh to-cloudrun <input> <output>
-./scripts/convert-env-format.sh to-appengine <input> <output>
+./scripts/integration-test.sh webhook   # Send test webhook
+./scripts/integration-test.sh verify    # Check dest repos
+./scripts/integration-test.sh full      # Both + wait
 ```
 
-**What it does:**
-- Converts between App Engine format (with `env_variables:` wrapper) and Cloud Run format (plain YAML)
-- Handles indentation automatically
-- Validates input file exists
-- Prompts before overwriting existing files
-
-**Example:**
-```bash
-# Convert App Engine → Cloud Run
-./scripts/convert-env-format.sh to-cloudrun env.yaml env-cloudrun.yaml
+**Environment:**
+- `APP_URL` — App URL (default: `http://localhost:8080`)
+- `WEBHOOK_SECRET` — Webhook secret (default: reads from `.env.test`)
+- `DEST_REPO_1`, `DEST_PATH_1` — First destination repo/path to verify
+- `DEST_REPO_2`, `DEST_PATH_2` — Second destination repo/path to verify
 
-# Convert Cloud Run → App Engine
-./scripts/convert-env-format.sh to-appengine env-cloudrun.yaml env.yaml
-```
+### test-slack.sh
 
-**Format differences:**
-```yaml
-# App Engine format (env.yaml)
-env_variables:
-  GITHUB_APP_ID: "123456"
-  REPO_OWNER: "mongodb"
+Test Slack notifications by sending example messages (success, error, deprecation).
 
-# Cloud Run format (env-cloudrun.yaml)
-GITHUB_APP_ID: "123456"
-REPO_OWNER: "mongodb"
+**Usage:**
+```bash
+./scripts/test-slack.sh [webhook-url]
+# Or: export SLACK_WEBHOOK_URL="https://hooks.slack.com/services/..."
 ```
 
-### test-with-pr.sh
+### diagnose-github-auth.sh
 
-Fetch real PR data from GitHub and send it to the webhook.
+Diagnostic script for GitHub App authentication issues. Checks Secret Manager, private key format, env config, and Cloud Run service health/readiness.
 
 **Usage:**
 ```bash
-./scripts/test-with-pr.sh <pr-number> <owner> <repo> [webhook-url]
+./scripts/diagnose-github-auth.sh
 ```
 
-**Arguments:**
-- `pr-number` - Pull request number (required)
-- `owner` - Repository owner (required)
-- `repo` - Repository name (required)
-- `webhook-url` - Webhook URL (optional, default: `http://localhost:8080/webhook`)
+### test-github-access.sh
 
-**Environment Variables:**
-- `GITHUB_TOKEN` - GitHub personal access token (required)
+Test if the deployed Cloud Run service can access the configured GitHub repository. Checks the `/ready` endpoint and recent logs for 401 errors.
 
-**Example:**
+**Usage:**
 ```bash
-# Set GitHub token
-export GITHUB_TOKEN=ghp_your_token_here
-
-# Test with real PR
-./scripts/test-with-pr.sh 42 mongodb docs-code-examples
-
-# Test with custom webhook URL
-./scripts/test-with-pr.sh 42 mongodb docs-code-examples http://localhost:8080/webhook
+./scripts/test-github-access.sh
 ```
 
-**Output:**
-```
-Fetching PR #42 from mongodb/docs-code-examples...
+### check-installation-repos.sh
 
-✓ PR fetched successfully
-✓ PR Title: Add Go database examples
-✓ Files changed: 21
-✓ Sending to webhook...
-✓ Response: 200 OK
+List all repositories accessible to a GitHub App installation. Generates a JWT, exchanges it for an installation token, and queries the GitHub API.
 
-Check application logs for processing details.
+**Usage:**
+```bash
+./scripts/check-installation-repos.sh
 ```
 
+**Requires:** `jq`, `ruby` with `jwt` gem, `gcloud`
+
 ## Common Workflows
 
 ### Local Development
 
 ```bash
-# 1. Start app locally
+# 1. Start app locally (dry-run + debug)
 ./scripts/run-local.sh
 
 # 2. In another terminal, test it
@@ -237,6 +160,12 @@ Check application logs for processing details.
 curl http://localhost:8080/metrics | jq
 ```
 
+### Pre-Push Validation
+
+```bash
+./scripts/ci-local.sh
+```
+
 ### Testing with Real Data
 
 ```bash
@@ -248,183 +177,30 @@ export GITHUB_TOKEN=ghp_...
 
 # 3. Test with real PR
 ./scripts/test-with-pr.sh 42 myorg myrepo
-
-# 4. Check results
-./scripts/test-and-check.sh
 ```
 
 ### Testing Slack Integration
 
 ```bash
-# 1. Test Slack webhook
 export SLACK_WEBHOOK_URL="https://hooks.slack.com/services/..."
 ./scripts/test-slack.sh
-
-# 2. Start app with Slack enabled
-./scripts/run-local.sh
-
-# 3. Send test webhook
-./scripts/test-and-check.sh
-
-# 4. Check Slack channel for notification
-```
-
-### Dry-Run Testing
-
-```bash
-# 1. Start app in dry-run mode
-DRY_RUN=true ./scripts/run-local.sh
-
-# 2. Test processing
-./scripts/test-and-check.sh
-
-# 3. Verify no commits were made (check logs)
-```
-
-## Script Details
-
-### Environment Variables
-
-All scripts respect these environment variables:
-
-**Application:**
-- `CONFIG_FILE` - Configuration file path
-- `DRY_RUN` - Enable dry-run mode
-- `LOG_LEVEL` - Logging level (debug, info, warn, error)
-- `COPIER_DISABLE_CLOUD_LOGGING` - Disable Google Cloud logging
-
-**GitHub:**
-- `GITHUB_TOKEN` - GitHub personal access token
-- `GITHUB_APP_ID` - GitHub App ID
-- `GITHUB_INSTALLATION_ID` - GitHub Installation ID
-
-**Slack:**
-- `SLACK_WEBHOOK_URL` - Slack webhook URL
-- `SLACK_CHANNEL` - Slack channel
-- `SLACK_ENABLED` - Enable/disable Slack notifications
-
-**MongoDB:**
-- `MONGO_URI` - MongoDB connection string
-- `AUDIT_ENABLED` - Enable/disable audit logging
-
-### Exit Codes
-
-All scripts use standard exit codes:
-- `0` - Success
-- `1` - Error occurred
-
-### Error Handling
-
-Scripts include error handling and will:
-- Display clear error messages
-- Exit with non-zero code on failure
-- Provide troubleshooting hints
-
-## Creating Custom Scripts
-
-### Template
-
-```bash
-#!/bin/bash
-
-# Script description
-# Usage: ./my-script.sh [args]
-
-set -e  # Exit on error
-
-# Colors for output
-GREEN='\033[0;32m'
-RED='\033[0;31m'
-NC='\033[0m' # No Color
-
-# Check prerequisites
-if [ -z "$REQUIRED_VAR" ]; then
-    echo -e "${RED}Error: REQUIRED_VAR not set${NC}"
-    exit 1
-fi
-
-# Main logic
-echo -e "${GREEN}Starting...${NC}"
-
-# Do work
-# ...
-
-echo -e "${GREEN}Complete!${NC}"
 ```
 
-### Best Practices
-
-1. **Use `set -e`** to exit on errors
-2. **Check prerequisites** before running
-3. **Provide clear output** with colors
-4. **Include usage instructions** in comments
-5. **Handle errors gracefully**
-6. **Make scripts executable**: `chmod +x script.sh`
+### Diagnosing Auth Issues
 
-## Troubleshooting
-
-### Script Not Executable
-
-**Error:**
-```
-Permission denied: ./scripts/run-local.sh
-```
-
-**Solution:**
 ```bash
-chmod +x scripts/*.sh
-```
+# Full diagnostic
+./scripts/diagnose-github-auth.sh
 
-### Environment Variables Not Set
-
-**Error:**
-```
-Error: GITHUB_TOKEN not set
-```
+# Check repo access
+./scripts/test-github-access.sh
 
-**Solution:**
-```bash
-export GITHUB_TOKEN=ghp_your_token_here
-# Or add to configs/.env.local
-```
-
-### App Not Running
-
-**Error:**
-```
-Connection refused
-```
-
-**Solution:**
-```bash
-# Start the app first
-./scripts/run-local.sh
-
-# Then run tests in another terminal
-```
-
-### Slack Webhook Fails
-
-**Error:**
-```
-Error: invalid_payload
-```
-
-**Solution:**
-```bash
-# Verify webhook URL
-echo $SLACK_WEBHOOK_URL
-
-# Test directly
-curl -X POST -H 'Content-type: application/json' \
-  --data '{"text":"Test"}' \
-  "$SLACK_WEBHOOK_URL"
+# List accessible repos
+./scripts/check-installation-repos.sh
 ```
 
 ## See Also
 
 - [Local Testing Guide](../docs/LOCAL-TESTING.md) - Local development
 - [Webhook Testing Guide](../docs/WEBHOOK-TESTING.md) - Testing webhooks
-- [Quick Reference](../docs/QUICK-REFERENCE.md) - All commands
 - [test-webhook Tool](../cmd/test-webhook/README.md) - Test webhook tool
-
diff --git a/scripts/check-installation-repos.sh b/scripts/check-installation-repos.sh
index a504c8d..ff4c68b 100755
--- a/scripts/check-installation-repos.sh
+++ b/scripts/check-installation-repos.sh
@@ -16,11 +16,20 @@ if ! command -v jq &> /dev/null; then
     exit 1
 fi
 
-# Get the installation ID from env.yaml
-INSTALLATION_ID=$(grep "INSTALLATION_ID:" env.yaml | grep -v "#" | awk '{print $2}' | tr -d '"')
+# Get the installation ID from env-cloudrun.yaml (or env.yaml fallback)
+ENV_FILE="env-cloudrun.yaml"
+if [ ! -f "$ENV_FILE" ]; then
+    ENV_FILE="env.yaml"
+fi
+if [ ! -f "$ENV_FILE" ]; then
+    echo "❌ Neither env-cloudrun.yaml nor env.yaml found"
+    exit 1
+fi
+
+INSTALLATION_ID=$(grep "INSTALLATION_ID:" "$ENV_FILE" | grep -v "#" | awk '{print $2}' | tr -d '"')
 
 if [ -z "$INSTALLATION_ID" ]; then
-    echo "❌ INSTALLATION_ID not found in env.yaml"
+    echo "❌ INSTALLATION_ID not found in $ENV_FILE"
     exit 1
 fi
 
@@ -39,11 +48,11 @@ fi
 echo "✅ Private key retrieved"
 echo ""
 
-# Get the GitHub App ID from env.yaml
-APP_ID=$(grep "GITHUB_APP_ID:" env.yaml | awk '{print $2}' | tr -d '"')
+# Get the GitHub App ID
+APP_ID=$(grep "GITHUB_APP_ID:" "$ENV_FILE" | awk '{print $2}' | tr -d '"')
 
 if [ -z "$APP_ID" ]; then
-    echo "❌ GITHUB_APP_ID not found in env.yaml"
+    echo "❌ GITHUB_APP_ID not found in $ENV_FILE"
     exit 1
 fi
 
diff --git a/scripts/ci-local.sh b/scripts/ci-local.sh
new file mode 100755
index 0000000..b983a4a
--- /dev/null
+++ b/scripts/ci-local.sh
@@ -0,0 +1,64 @@
+#!/bin/bash
+
+# Run the full CI pipeline locally before pushing
+# Mirrors what .github/workflows/ci.yml does
+#
+# Usage: ./scripts/ci-local.sh
+
+set -e
+
+# Colors
+GREEN='\033[0;32m'
+RED='\033[0;31m'
+BLUE='\033[0;34m'
+NC='\033[0m' # No Color
+
+PASS="${GREEN}PASS${NC}"
+FAIL="${RED}FAIL${NC}"
+
+echo -e "${BLUE}Running local CI pipeline...${NC}"
+echo ""
+
+# 1. Build
+echo -n "Build...        "
+if go build ./... 2>&1; then
+    echo -e "$PASS"
+else
+    echo -e "$FAIL"
+    exit 1
+fi
+
+# 2. Test with race detector
+echo -n "Test (race)...  "
+if go test -race ./... 2>&1; then
+    echo -e "$PASS"
+else
+    echo -e "$FAIL"
+    exit 1
+fi
+
+# 3. Lint
+echo -n "Lint...         "
+if command -v golangci-lint &> /dev/null; then
+    if golangci-lint run ./... 2>&1; then
+        echo -e "$PASS"
+    else
+        echo -e "$FAIL"
+        exit 1
+    fi
+else
+    echo -e "${RED}SKIP${NC} (golangci-lint not installed)"
+    echo "  Install: go install github.com/golangci/golangci-lint/cmd/golangci-lint@latest"
+fi
+
+# 4. Vet
+echo -n "Vet...          "
+if go vet ./... 2>&1; then
+    echo -e "$PASS"
+else
+    echo -e "$FAIL"
+    exit 1
+fi
+
+echo ""
+echo -e "${GREEN}All checks passed!${NC}"
diff --git a/scripts/convert-env-format.sh b/scripts/convert-env-format.sh
deleted file mode 100755
index 44bf7b9..0000000
--- a/scripts/convert-env-format.sh
+++ /dev/null
@@ -1,101 +0,0 @@
-#!/bin/bash
-
-# Convert between App Engine (env.yaml) and Cloud Run (env-cloudrun.yaml) formats
-#
-# Usage:
-#   ./convert-env-format.sh to-cloudrun env.yaml env-cloudrun.yaml
-#   ./convert-env-format.sh to-appengine env-cloudrun.yaml env.yaml
-
-set -e
-
-# Colors for output
-RED='\033[0;31m'
-GREEN='\033[0;32m'
-BLUE='\033[0;34m'
-YELLOW='\033[1;33m'
-NC='\033[0m' # No Color
-
-# Print usage
-usage() {
-    echo "Convert between App Engine and Cloud Run environment file formats"
-    echo ""
-    echo "Usage:"
-    echo "  $0 to-cloudrun <input-env.yaml> <output-env-cloudrun.yaml>"
-    echo "  $0 to-appengine <input-env-cloudrun.yaml> <output-env.yaml>"
-    echo ""
-    echo "Examples:"
-    echo "  # Convert App Engine format to Cloud Run format"
-    echo "  $0 to-cloudrun env.yaml env-cloudrun.yaml"
-    echo ""
-    echo "  # Convert Cloud Run format to App Engine format"
-    echo "  $0 to-appengine env-cloudrun.yaml env.yaml"
-    echo ""
-    echo "Formats:"
-    echo "  App Engine:   env_variables: wrapper with indented keys"
-    echo "  Cloud Run:    Plain YAML without wrapper"
-    exit 1
-}
-
-# Check arguments
-if [ $# -ne 3 ]; then
-    usage
-fi
-
-COMMAND=$1
-INPUT=$2
-OUTPUT=$3
-
-# Validate command
-if [ "$COMMAND" != "to-cloudrun" ] && [ "$COMMAND" != "to-appengine" ]; then
-    echo -e "${RED}Error: Invalid command '$COMMAND'${NC}"
-    echo "Must be 'to-cloudrun' or 'to-appengine'"
-    usage
-fi
-
-# Check input file exists
-if [ ! -f "$INPUT" ]; then
-    echo -e "${RED}Error: Input file '$INPUT' not found${NC}"
-    exit 1
-fi
-
-# Check if output file exists
-if [ -f "$OUTPUT" ]; then
-    echo -e "${YELLOW}Warning: Output file '$OUTPUT' already exists${NC}"
-    read -p "Overwrite? (y/N) " -n 1 -r
-    echo
-    if [[ ! $REPLY =~ ^[Yy]$ ]]; then
-        echo "Aborted"
-        exit 1
-    fi
-fi
-
-# Convert to Cloud Run format (remove env_variables wrapper and unindent)
-if [ "$COMMAND" = "to-cloudrun" ]; then
-    echo -e "${BLUE}Converting App Engine format to Cloud Run format...${NC}"
-    
-    # Remove 'env_variables:' line and unindent by 2 spaces
-    sed '/^env_variables:/d' "$INPUT" | sed 's/^  //' > "$OUTPUT"
-    
-    echo -e "${GREEN}✓ Converted to Cloud Run format: $OUTPUT${NC}"
-    echo ""
-    echo "Deploy with:"
-    echo "  gcloud run deploy examples-copier --source . --env-vars-file=$OUTPUT"
-fi
-
-# Convert to App Engine format (add env_variables wrapper and indent)
-if [ "$COMMAND" = "to-appengine" ]; then
-    echo -e "${BLUE}Converting Cloud Run format to App Engine format...${NC}"
-    
-    # Add 'env_variables:' header and indent all lines by 2 spaces
-    echo "env_variables:" > "$OUTPUT"
-    sed 's/^/  /' "$INPUT" >> "$OUTPUT"
-    
-    echo -e "${GREEN}✓ Converted to App Engine format: $OUTPUT${NC}"
-    echo ""
-    echo "Deploy with:"
-    echo "  gcloud app deploy app.yaml  # Includes $OUTPUT automatically"
-fi
-
-echo ""
-echo -e "${YELLOW}Note: Review the output file before deploying!${NC}"
-
diff --git a/scripts/convert-env-to-yaml.sh b/scripts/convert-env-to-yaml.sh
deleted file mode 100755
index 3a41ace..0000000
--- a/scripts/convert-env-to-yaml.sh
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/bin/bash
-# Convert .env file to env.yaml format for Google Cloud App Engine
-
-set -e
-
-# Default input/output files
-INPUT_FILE="${1:-.env}"
-OUTPUT_FILE="${2:-env.yaml}"
-
-if [ ! -f "$INPUT_FILE" ]; then
-    echo "Error: Input file '$INPUT_FILE' not found"
-    echo "Usage: $0 [input-file] [output-file]"
-    echo "Example: $0 .env.production env.yaml"
-    exit 1
-fi
-
-echo "Converting $INPUT_FILE to $OUTPUT_FILE..."
-
-# Start the YAML file
-echo "env_variables:" > "$OUTPUT_FILE"
-
-# Read the .env file and convert to YAML
-while IFS= read -r line || [ -n "$line" ]; do
-    # Skip empty lines and comments
-    if [[ -z "$line" ]] || [[ "$line" =~ ^[[:space:]]*# ]]; then
-        continue
-    fi
-    
-    # Extract key and value
-    if [[ "$line" =~ ^([^=]+)=(.*)$ ]]; then
-        key="${BASH_REMATCH[1]}"
-        value="${BASH_REMATCH[2]}"
-        
-        # Remove leading/trailing whitespace from key
-        key=$(echo "$key" | sed 's/^[[:space:]]*//;s/[[:space:]]*$//')
-        
-        # Remove quotes from value if present
-        value=$(echo "$value" | sed 's/^["'\'']\(.*\)["'\'']$/\1/')
-        
-        # Write to YAML file with proper indentation
-        echo "  $key: \"$value\"" >> "$OUTPUT_FILE"
-    fi
-done < "$INPUT_FILE"
-
-echo "✅ Conversion complete: $OUTPUT_FILE"
-echo ""
-echo "⚠️  IMPORTANT: Review $OUTPUT_FILE before deploying!"
-echo "   - Verify all values are correct"
-echo "   - Check for sensitive data"
-echo "   - Ensure $OUTPUT_FILE is in .gitignore"
-
diff --git a/scripts/deploy-cloudrun.sh b/scripts/deploy-cloudrun.sh
index 7052b96..4f885f3 100755
--- a/scripts/deploy-cloudrun.sh
+++ b/scripts/deploy-cloudrun.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# Deploy examples-copier to Google Cloud Run
+# Deploy github-copier to Google Cloud Run
 # Usage: ./scripts/deploy-cloudrun.sh [region]
 
 set -e
diff --git a/scripts/diagnose-github-auth.sh b/scripts/diagnose-github-auth.sh
index e6c89f9..dc38a28 100755
--- a/scripts/diagnose-github-auth.sh
+++ b/scripts/diagnose-github-auth.sh
@@ -5,7 +5,7 @@
 
 set -e
 
-echo "🔍 GitHub App Authentication Diagnostics"
+echo "GitHub App Authentication Diagnostics"
 echo "=========================================="
 echo ""
 
@@ -17,58 +17,59 @@ NC='\033[0m' # No Color
 
 # Check if gcloud is installed
 if ! command -v gcloud &> /dev/null; then
-    echo -e "${RED}❌ gcloud CLI not found${NC}"
+    echo -e "${RED}gcloud CLI not found${NC}"
     echo "Please install: https://cloud.google.com/sdk/docs/install"
     exit 1
 fi
 
-echo -e "${GREEN}✅ gcloud CLI found${NC}"
+echo -e "${GREEN}gcloud CLI found${NC}"
 
 # Get project info
 PROJECT_ID=$(gcloud config get-value project 2>/dev/null)
 if [ -z "$PROJECT_ID" ]; then
-    echo -e "${RED}❌ No GCP project set${NC}"
+    echo -e "${RED}No GCP project set${NC}"
     echo "Run: gcloud config set project YOUR_PROJECT_ID"
     exit 1
 fi
 
-echo -e "${GREEN}✅ GCP Project: $PROJECT_ID${NC}"
+echo -e "${GREEN}GCP Project: $PROJECT_ID${NC}"
 
 PROJECT_NUMBER=$(gcloud projects describe "$PROJECT_ID" --format="value(projectNumber)")
-echo -e "${GREEN}✅ Project Number: $PROJECT_NUMBER${NC}"
+echo -e "${GREEN}Project Number: $PROJECT_NUMBER${NC}"
 
-SERVICE_ACCOUNT="${PROJECT_NUMBER}@appspot.gserviceaccount.com"
+# Cloud Run uses the default Compute Engine SA unless a custom SA is configured
+SERVICE_ACCOUNT="${PROJECT_NUMBER}-compute@developer.gserviceaccount.com"
 echo -e "   Service Account: $SERVICE_ACCOUNT"
 echo ""
 
 # Check Secret Manager API
-echo "📦 Checking Secret Manager..."
+echo "Checking Secret Manager..."
 if gcloud services list --enabled --filter="name:secretmanager.googleapis.com" --format="value(name)" | grep -q secretmanager; then
-    echo -e "${GREEN}✅ Secret Manager API enabled${NC}"
+    echo -e "${GREEN}Secret Manager API enabled${NC}"
 else
-    echo -e "${RED}❌ Secret Manager API not enabled${NC}"
+    echo -e "${RED}Secret Manager API not enabled${NC}"
     echo "Run: gcloud services enable secretmanager.googleapis.com"
     exit 1
 fi
 
 # Check if secrets exist
 echo ""
-echo "🔐 Checking Secrets..."
+echo "Checking Secrets..."
 
 check_secret() {
     local secret_name=$1
     if gcloud secrets describe "$secret_name" &>/dev/null; then
-        echo -e "${GREEN}✅ Secret exists: $secret_name${NC}"
+        echo -e "${GREEN}Secret exists: $secret_name${NC}"
         
         # Check IAM permissions
         if gcloud secrets get-iam-policy "$secret_name" --format="value(bindings.members)" | grep -q "$SERVICE_ACCOUNT"; then
-            echo -e "${GREEN}   ✅ Service account has access${NC}"
+            echo -e "${GREEN}   Service account has access${NC}"
         else
-            echo -e "${RED}   ❌ Service account does NOT have access${NC}"
+            echo -e "${RED}   Service account does NOT have access${NC}"
             echo -e "${YELLOW}   Fix: gcloud secrets add-iam-policy-binding $secret_name --member=\"serviceAccount:${SERVICE_ACCOUNT}\" --role=\"roles/secretmanager.secretAccessor\"${NC}"
         fi
     else
-        echo -e "${RED}❌ Secret NOT found: $secret_name${NC}"
+        echo -e "${RED}Secret NOT found: $secret_name${NC}"
     fi
 }
 
@@ -77,98 +78,110 @@ check_secret "webhook-secret"
 
 # Check if we can access the PEM key
 echo ""
-echo "🔑 Checking GitHub App Private Key..."
+echo "Checking GitHub App Private Key..."
 if gcloud secrets versions access latest --secret=CODE_COPIER_PEM &>/dev/null; then
     PEM_FIRST_LINE=$(gcloud secrets versions access latest --secret=CODE_COPIER_PEM | head -n 1)
     if [[ "$PEM_FIRST_LINE" == "-----BEGIN RSA PRIVATE KEY-----" ]] || [[ "$PEM_FIRST_LINE" == "-----BEGIN PRIVATE KEY-----" ]]; then
-        echo -e "${GREEN}✅ Private key format looks correct${NC}"
+        echo -e "${GREEN}Private key format looks correct${NC}"
     else
-        echo -e "${RED}❌ Private key format looks incorrect${NC}"
+        echo -e "${RED}Private key format looks incorrect${NC}"
         echo "   First line: $PEM_FIRST_LINE"
     fi
 else
-    echo -e "${RED}❌ Cannot access private key${NC}"
+    echo -e "${RED}Cannot access private key${NC}"
 fi
 
-# Check env.yaml
+# Check env-cloudrun.yaml
 echo ""
-echo "⚙️  Checking env.yaml configuration..."
-if [ -f "env.yaml" ]; then
-    echo -e "${GREEN}✅ env.yaml found${NC}"
+echo "Checking env-cloudrun.yaml configuration..."
+ENV_FILE="env-cloudrun.yaml"
+if [ -f "$ENV_FILE" ]; then
+    echo -e "${GREEN}$ENV_FILE found${NC}"
     
-    # Extract values
-    GITHUB_APP_ID=$(grep "GITHUB_APP_ID:" env.yaml | awk '{print $2}' | tr -d '"')
-    INSTALLATION_ID=$(grep "INSTALLATION_ID:" env.yaml | grep -v "#" | awk '{print $2}' | tr -d '"')
-    REPO_OWNER=$(grep "REPO_OWNER:" env.yaml | grep -v "#" | awk '{print $2}' | tr -d '"')
-    REPO_NAME=$(grep "REPO_NAME:" env.yaml | grep -v "#" | awk '{print $2}' | tr -d '"')
+    # Extract values (plain YAML, no env_variables wrapper)
+    GITHUB_APP_ID=$(grep "GITHUB_APP_ID:" "$ENV_FILE" | awk '{print $2}' | tr -d '"')
+    INSTALLATION_ID=$(grep "INSTALLATION_ID:" "$ENV_FILE" | grep -v "#" | awk '{print $2}' | tr -d '"')
+    REPO_OWNER=$(grep "REPO_OWNER:" "$ENV_FILE" | grep -v "#" | awk '{print $2}' | tr -d '"')
+    REPO_NAME=$(grep "REPO_NAME:" "$ENV_FILE" | grep -v "#" | awk '{print $2}' | tr -d '"')
     
     echo "   GitHub App ID: $GITHUB_APP_ID"
     echo "   Installation ID: $INSTALLATION_ID"
     echo "   Repository: $REPO_OWNER/$REPO_NAME"
     
-    if [ -z "$GITHUB_APP_ID" ] || [ -z "$INSTALLATION_ID" ] || [ -z "$REPO_OWNER" ] || [ -z "$REPO_NAME" ]; then
-        echo -e "${RED}❌ Missing required configuration${NC}"
+    if [ -z "$GITHUB_APP_ID" ] || [ -z "$REPO_OWNER" ] || [ -z "$REPO_NAME" ]; then
+        echo -e "${RED}Missing required configuration${NC}"
     else
-        echo -e "${GREEN}✅ Configuration looks complete${NC}"
+        echo -e "${GREEN}Configuration looks complete${NC}"
     fi
 else
-    echo -e "${RED}❌ env.yaml not found${NC}"
+    echo -e "${RED}$ENV_FILE not found${NC}"
+    echo "Create it: cp configs/env.yaml.production env-cloudrun.yaml"
 fi
 
-# Check App Engine deployment
+# Check Cloud Run deployment
 echo ""
-echo "🚀 Checking App Engine deployment..."
-if gcloud app describe &>/dev/null; then
-    APP_URL=$(gcloud app describe --format="value(defaultHostname)")
-    echo -e "${GREEN}✅ App Engine app exists${NC}"
-    echo "   URL: https://$APP_URL"
+echo "Checking Cloud Run deployment..."
+SERVICE_URL=$(gcloud run services describe github-copier --format="value(status.url)" 2>/dev/null)
+if [ -n "$SERVICE_URL" ]; then
+    echo -e "${GREEN}Cloud Run service exists${NC}"
+    echo "   URL: $SERVICE_URL"
     
     # Try to hit health endpoint
     echo ""
-    echo "🏥 Checking health endpoint..."
-    if curl -s -f "https://$APP_URL/health" &>/dev/null; then
-        echo -e "${GREEN}✅ Health endpoint responding${NC}"
-        curl -s "https://$APP_URL/health" | python3 -m json.tool 2>/dev/null || echo ""
+    echo "Checking health endpoint..."
+    if curl -s -f "$SERVICE_URL/health" &>/dev/null; then
+        echo -e "${GREEN}Health endpoint responding${NC}"
+        curl -s "$SERVICE_URL/health" | python3 -m json.tool 2>/dev/null || echo ""
     else
-        echo -e "${RED}❌ Health endpoint not responding${NC}"
+        echo -e "${RED}Health endpoint not responding${NC}"
+    fi
+
+    echo ""
+    echo "Checking readiness endpoint..."
+    if curl -s -f "$SERVICE_URL/ready" &>/dev/null; then
+        echo -e "${GREEN}Readiness endpoint responding${NC}"
+        curl -s "$SERVICE_URL/ready" | python3 -m json.tool 2>/dev/null || echo ""
+    else
+        echo -e "${YELLOW}Readiness endpoint returned non-200 (may indicate auth or connectivity issue)${NC}"
+        curl -s "$SERVICE_URL/ready" | python3 -m json.tool 2>/dev/null || echo ""
     fi
 else
-    echo -e "${YELLOW}⚠️  No App Engine app deployed yet${NC}"
+    echo -e "${YELLOW}No Cloud Run service 'github-copier' found${NC}"
 fi
 
 # Summary
 echo ""
-echo "📋 Summary & Next Steps"
+echo "Summary & Next Steps"
 echo "======================="
 echo ""
 
 # Check for common issues
 ISSUES_FOUND=0
 
-if ! gcloud secrets get-iam-policy CODE_COPIER_PEM --format="value(bindings.members)" | grep -q "$SERVICE_ACCOUNT"; then
-    echo -e "${RED}❌ Issue: Service account doesn't have access to CODE_COPIER_PEM${NC}"
+if ! gcloud secrets get-iam-policy CODE_COPIER_PEM --format="value(bindings.members)" 2>/dev/null | grep -q "$SERVICE_ACCOUNT"; then
+    echo -e "${RED}Issue: Service account doesn't have access to CODE_COPIER_PEM${NC}"
     echo "   Fix: Run ./scripts/grant-secret-access.sh"
     ISSUES_FOUND=$((ISSUES_FOUND + 1))
 fi
 
-if [ ! -f "env.yaml" ]; then
-    echo -e "${RED}❌ Issue: env.yaml not found${NC}"
-    echo "   Fix: cp configs/env.yaml.example env.yaml && nano env.yaml"
+if [ ! -f "$ENV_FILE" ]; then
+    echo -e "${RED}Issue: $ENV_FILE not found${NC}"
+    echo "   Fix: cp configs/env.yaml.production env-cloudrun.yaml && nano env-cloudrun.yaml"
     ISSUES_FOUND=$((ISSUES_FOUND + 1))
 fi
 
 if [ $ISSUES_FOUND -eq 0 ]; then
-    echo -e "${GREEN}✅ No obvious issues found${NC}"
+    echo -e "${GREEN}No obvious issues found${NC}"
     echo ""
     echo "If you're still seeing 401 errors, check:"
     echo "1. GitHub App is installed on the repository: https://github.com/settings/installations"
     echo "2. Installation ID matches the repository"
     echo "3. Private key in Secret Manager matches the GitHub App"
-    echo "4. GitHub App has 'Contents' read permission"
+    echo "4. GitHub App has 'Contents' write and 'Pull requests' write permissions"
+    echo "   (see github-app-manifest.yml for required permissions)"
     echo ""
-    echo "View logs: gcloud app logs tail -s default"
+    echo "View logs: gcloud run services logs read github-copier --limit=50"
 else
     echo ""
     echo -e "${YELLOW}Found $ISSUES_FOUND issue(s) - please fix them and try again${NC}"
 fi
-
diff --git a/scripts/grant-secret-access.sh b/scripts/grant-secret-access.sh
index 023832c..d08cc8a 100755
--- a/scripts/grant-secret-access.sh
+++ b/scripts/grant-secret-access.sh
@@ -1,13 +1,20 @@
 #!/bin/bash
-# Grant App Engine access to all secrets
+# Grant Cloud Run service account access to all secrets
+#
+# NOTE: If you use a custom service account for Cloud Run (recommended),
+# update SERVICE_ACCOUNT below to match. The default Compute Engine SA
+# is used here as a baseline.
 
 set -e
 
 PROJECT_ID="github-copy-code-examples"
 PROJECT_NUMBER="1054147886816"
-SERVICE_ACCOUNT="${PROJECT_NUMBER}@appspot.gserviceaccount.com"
 
-echo "Granting App Engine service account access to secrets..."
+# Cloud Run uses the default Compute Engine service account unless a custom SA is configured.
+# Previously this script incorrectly targeted the App Engine SA (${PROJECT_NUMBER}@appspot.gserviceaccount.com).
+SERVICE_ACCOUNT="${PROJECT_NUMBER}-compute@developer.gserviceaccount.com"
+
+echo "Granting Cloud Run service account access to secrets..."
 echo "Service Account: ${SERVICE_ACCOUNT}"
 echo ""
 
@@ -27,7 +34,7 @@ for SECRET in "${SECRETS[@]}"; do
   echo ""
 done
 
-echo "✅ Done! Verifying permissions..."
+echo "Done! Verifying permissions..."
 echo ""
 
 for SECRET in "${SECRETS[@]}"; do
@@ -38,5 +45,4 @@ for SECRET in "${SECRETS[@]}"; do
   echo ""
 done
 
-echo "✅ All secrets are now accessible by App Engine!"
-
+echo "All secrets are now accessible by Cloud Run!"
diff --git a/scripts/integration-test.sh b/scripts/integration-test.sh
index 1914487..9f5e9d9 100755
--- a/scripts/integration-test.sh
+++ b/scripts/integration-test.sh
@@ -69,7 +69,7 @@ send_webhook() {
     log_info "Signature: $signature"
     
     response=$(curl -s -w "\n%{http_code}" \
-        -X POST "$APP_URL/webhook" \
+        -X POST "$APP_URL/events" \
         -H "Content-Type: application/json" \
         -H "X-GitHub-Event: pull_request" \
         -H "X-Hub-Signature-256: $signature" \
@@ -117,16 +117,17 @@ main() {
             ;;
         verify)
             log_info "Verifying destination repos..."
-            verify_dest_repo "cbullinger/copier-app-dest-1" "go-examples"
-            verify_dest_repo "cbullinger/copier-app-dest-2" "python-examples"
+            # Update these to match your test workflow destinations
+            verify_dest_repo "${DEST_REPO_1:-your-org/dest-repo-1}" "${DEST_PATH_1:-examples}"
+            verify_dest_repo "${DEST_REPO_2:-your-org/dest-repo-2}" "${DEST_PATH_2:-examples}"
             ;;
         full)
             check_app || exit 1
             send_webhook "$PAYLOAD_FILE"
             log_info "Waiting 10s for processing..."
             sleep 10
-            verify_dest_repo "cbullinger/copier-app-dest-1" "go-examples"
-            verify_dest_repo "cbullinger/copier-app-dest-2" "python-examples"
+            verify_dest_repo "${DEST_REPO_1:-your-org/dest-repo-1}" "${DEST_PATH_1:-examples}"
+            verify_dest_repo "${DEST_REPO_2:-your-org/dest-repo-2}" "${DEST_PATH_2:-examples}"
             ;;
         *)
             echo "Usage: $0 [webhook|verify|full]"
diff --git a/scripts/run-local.sh b/scripts/run-local.sh
index 88df337..663cced 100755
--- a/scripts/run-local.sh
+++ b/scripts/run-local.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 
-# Run examples-copier locally with proper development settings
+# Run github-copier locally with proper development settings
 # This script sets up the environment for local testing
 
 set -e
@@ -11,14 +11,14 @@ BLUE='\033[0;34m'
 YELLOW='\033[1;33m'
 NC='\033[0m' # No Color
 
-echo -e "${BLUE}Starting examples-copier in local development mode${NC}"
+echo -e "${BLUE}Starting github-copier in local development mode${NC}"
 echo ""
 
 # Check if binary exists
-if [ ! -f "./examples-copier" ]; then
-    echo -e "${YELLOW}Building examples-copier...${NC}"
-    go build -o examples-copier .
-    echo -e "${GREEN}✓ Built examples-copier${NC}"
+if [ ! -f "./github-copier" ]; then
+    echo -e "${YELLOW}Building github-copier...${NC}"
+    go build -o github-copier .
+    echo -e "${GREEN}✓ Built github-copier${NC}"
 fi
 
 # Set local development environment
@@ -30,8 +30,8 @@ export METRICS_ENABLED=true
 export PORT=8080
 export AUDIT_ENABLED=false
 
-# Use copier-copier-config.yaml by default (or override)
-export CONFIG_FILE=${CONFIG_FILE:-copier-copier-config.yaml}
+# Use copier-config.yaml by default (or override)
+export CONFIG_FILE=${CONFIG_FILE:-copier-config.yaml}
 export DEPRECATION_FILE=${DEPRECATION_FILE:-deprecated_examples.json}
 
 # Load .env if it exists
@@ -64,5 +64,5 @@ echo -e "${BLUE}Press Ctrl+C to stop${NC}"
 echo ""
 
 # Run the application
-./examples-copier
+./github-copier
 
diff --git a/scripts/test-github-access.sh b/scripts/test-github-access.sh
index 9b8a7d7..3d47727 100755
--- a/scripts/test-github-access.sh
+++ b/scripts/test-github-access.sh
@@ -1,76 +1,100 @@
 #!/bin/bash
 
 # Test if the GitHub App can access the configured repository
-# This script checks the recent logs for 401 errors
+# Checks the deployed Cloud Run service health and recent logs for errors
 
 set -e
 
-echo "🔍 Testing GitHub Repository Access"
+echo "Testing GitHub Repository Access"
 echo "===================================="
 echo ""
 
-# Get configuration from env.yaml
-REPO_OWNER=$(grep "REPO_OWNER:" env.yaml | grep -v "#" | awk '{print $2}' | tr -d '"')
-REPO_NAME=$(grep "REPO_NAME:" env.yaml | grep -v "#" | awk '{print $2}' | tr -d '"')
-INSTALLATION_ID=$(grep "INSTALLATION_ID:" env.yaml | grep -v "#" | awk '{print $2}' | tr -d '"')
+# Colors
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+NC='\033[0m' # No Color
+
+# Get configuration from env-cloudrun.yaml
+ENV_FILE="env-cloudrun.yaml"
+if [ ! -f "$ENV_FILE" ]; then
+    echo -e "${RED}$ENV_FILE not found${NC}"
+    echo "Create it: cp configs/env.yaml.production env-cloudrun.yaml"
+    exit 1
+fi
+
+REPO_OWNER=$(grep "REPO_OWNER:" "$ENV_FILE" | grep -v "#" | awk '{print $2}' | tr -d '"')
+REPO_NAME=$(grep "REPO_NAME:" "$ENV_FILE" | grep -v "#" | awk '{print $2}' | tr -d '"')
+INSTALLATION_ID=$(grep "INSTALLATION_ID:" "$ENV_FILE" | grep -v "#" | awk '{print $2}' | tr -d '"')
 
 echo "Configuration:"
 echo "  Repository: $REPO_OWNER/$REPO_NAME"
 echo "  Installation ID: $INSTALLATION_ID"
 echo ""
 
+# Get Cloud Run service URL
+SERVICE_URL=$(gcloud run services describe github-copier --format="value(status.url)" 2>/dev/null)
+if [ -z "$SERVICE_URL" ]; then
+    echo -e "${RED}Cloud Run service 'github-copier' not found${NC}"
+    exit 1
+fi
+
+echo "Service URL: $SERVICE_URL"
+echo ""
+
 # Check health endpoint
-echo "📊 Checking application health..."
-HEALTH=$(curl -s https://github-copy-code-examples.ue.r.appspot.com/health)
-AUTH_STATUS=$(echo "$HEALTH" | python3 -c "import sys, json; print(json.load(sys.stdin)['github']['authenticated'])")
+echo "Checking application health..."
+HEALTH=$(curl -s "$SERVICE_URL/health")
+echo "$HEALTH" | python3 -m json.tool 2>/dev/null || echo "$HEALTH"
+echo ""
+
+# Check readiness (includes GitHub auth check)
+echo "Checking readiness (includes GitHub auth)..."
+READY_CODE=$(curl -s -o /dev/null -w "%{http_code}" "$SERVICE_URL/ready")
+READY_BODY=$(curl -s "$SERVICE_URL/ready")
 
-if [ "$AUTH_STATUS" == "True" ]; then
-    echo "✅ GitHub authentication is working"
+if [ "$READY_CODE" == "200" ]; then
+    echo -e "${GREEN}Readiness check passed (HTTP $READY_CODE)${NC}"
+    echo "$READY_BODY" | python3 -m json.tool 2>/dev/null || echo "$READY_BODY"
 else
-    echo "❌ GitHub authentication is NOT working"
-    exit 1
+    echo -e "${RED}Readiness check failed (HTTP $READY_CODE)${NC}"
+    echo "$READY_BODY" | python3 -m json.tool 2>/dev/null || echo "$READY_BODY"
 fi
 echo ""
 
-# Check recent logs for 401 errors
-echo "🔍 Checking recent logs for 401 errors..."
-RECENT_ERRORS=$(gcloud logging read "resource.type=gae_app AND severity>=ERROR AND textPayload=~'401 Bad credentials'" --limit=5 --format="value(timestamp,textPayload)" --freshness=30m 2>/dev/null)
+# Check recent logs for errors
+echo "Checking recent logs for errors..."
+RECENT_ERRORS=$(gcloud run services logs read github-copier --limit=20 2>/dev/null | grep -i "401\|bad credentials\|unauthorized" || true)
 
 if [ -z "$RECENT_ERRORS" ]; then
-    echo "✅ No recent 401 errors found!"
-    echo ""
-    echo "🎉 GitHub App can successfully access the repository!"
+    echo -e "${GREEN}No recent 401 errors found${NC}"
 else
-    echo "❌ Found recent 401 errors:"
-    echo ""
+    echo -e "${RED}Found recent authentication errors:${NC}"
     echo "$RECENT_ERRORS"
     echo ""
-    echo "This means the GitHub App cannot access one or more repositories."
-    echo ""
     echo "Possible causes:"
     echo "1. GitHub App is not installed on the repository"
     echo "2. Installation ID doesn't match the repository"
-    echo "3. GitHub App doesn't have 'Contents' read permission"
+    echo "3. GitHub App private key is incorrect or expired"
+    echo "4. GitHub App doesn't have required permissions (see github-app-manifest.yml)"
     echo ""
     echo "To fix:"
     echo "1. Go to: https://github.com/settings/installations"
     echo "2. Find your GitHub App installation"
     echo "3. Make sure $REPO_OWNER/$REPO_NAME is in the list of accessible repositories"
-    echo "4. If not, click 'Configure' and add it"
 fi
 
 echo ""
-echo "📋 Summary"
+echo "Summary"
 echo "=========="
 echo "Repository: $REPO_OWNER/$REPO_NAME"
 echo "Installation ID: $INSTALLATION_ID"
-echo "Authentication: $AUTH_STATUS"
+echo "Readiness: HTTP $READY_CODE"
 
-if [ -z "$RECENT_ERRORS" ]; then
-    echo "Status: ✅ WORKING"
+if [ "$READY_CODE" == "200" ] && [ -z "$RECENT_ERRORS" ]; then
+    echo -e "Status: ${GREEN}WORKING${NC}"
     exit 0
 else
-    echo "Status: ❌ NEEDS ATTENTION"
+    echo -e "Status: ${RED}NEEDS ATTENTION${NC}"
     exit 1
 fi
-
diff --git a/scripts/test-slack.sh b/scripts/test-slack.sh
index 1cf5b0f..1e7a25e 100755
--- a/scripts/test-slack.sh
+++ b/scripts/test-slack.sh
@@ -38,7 +38,7 @@ echo ""
 # Test 1: Simple message
 echo -e "${BLUE}Test 1: Sending simple test message...${NC}"
 curl -X POST -H 'Content-type: application/json' \
-    --data '{"text":"🧪 Test message from examples-copier"}' \
+    --data '{"text":"🧪 Test message from github-copier"}' \
     "$WEBHOOK_URL"
 echo ""
 echo -e "${GREEN}✓ Simple message sent${NC}"
diff --git a/scripts/test-with-pr.sh b/scripts/test-with-pr.sh
index 01805e3..38d9a19 100755
--- a/scripts/test-with-pr.sh
+++ b/scripts/test-with-pr.sh
@@ -16,7 +16,7 @@ NC='\033[0m' # No Color
 PR_NUMBER=${1:-}
 OWNER=${2:-${REPO_OWNER:-}}
 REPO=${3:-${REPO_NAME:-}}
-WEBHOOK_URL=${WEBHOOK_URL:-http://localhost:8080/webhook}
+WEBHOOK_URL=${WEBHOOK_URL:-http://localhost:8080/events}
 WEBHOOK_SECRET=${WEBHOOK_SECRET:-}
 
 # Help message
@@ -32,7 +32,7 @@ if [ "$1" == "-h" ] || [ "$1" == "--help" ] || [ -z "$PR_NUMBER" ]; then
     echo ""
     echo "Environment Variables:"
     echo "  GITHUB_TOKEN      GitHub token for API access (required)"
-    echo "  WEBHOOK_URL       Webhook endpoint (default: http://localhost:8080/webhook)"
+    echo "  WEBHOOK_URL       Webhook endpoint (default: http://localhost:8080/events)"
     echo "  WEBHOOK_SECRET    Webhook secret for signature"
     echo "  REPO_OWNER        Default repository owner"
     echo "  REPO_NAME         Default repository name"
@@ -45,7 +45,7 @@ if [ "$1" == "-h" ] || [ "$1" == "--help" ] || [ -z "$PR_NUMBER" ]; then
     echo "  $0 123 myorg myrepo"
     echo ""
     echo "  # Test against production"
-    echo "  WEBHOOK_URL=https://myapp.appspot.com/webhook $0 123"
+    echo "  WEBHOOK_URL=https://your-service.run.app/events $0 123"
     echo ""
     exit 0
 fi
@@ -81,7 +81,7 @@ if [[ "$WEBHOOK_URL" == http://localhost* ]]; then
     echo -e "${BLUE}Checking if application is running...${NC}"
     if ! curl -s -f "$WEBHOOK_URL" > /dev/null 2>&1; then
         echo -e "${YELLOW}Warning: Application doesn't seem to be running at $WEBHOOK_URL${NC}"
-        echo -e "${YELLOW}Start it with: DRY_RUN=true ./examples-copier${NC}"
+        echo -e "${YELLOW}Start it with: DRY_RUN=true ./github-copier${NC}"
         read -p "Continue anyway? (y/N) " -n 1 -r
         echo
         if [[ ! $REPLY =~ ^[Yy]$ ]]; then
@@ -144,6 +144,6 @@ echo ""
 echo -e "${GREEN}✓ Test complete!${NC}"
 echo ""
 echo "Check application logs for processing details:"
-echo "  Local: Check terminal output"
-echo "  GCP: gcloud app logs tail -s default"
+echo "  Local: Check terminal output (JSON via slog)"
+echo "  Cloud Run: gcloud run services logs read github-copier --limit=50"
 
diff --git a/scripts/validate-config-detailed.py b/scripts/validate-config-detailed.py
deleted file mode 100755
index be7d415..0000000
--- a/scripts/validate-config-detailed.py
+++ /dev/null
@@ -1,171 +0,0 @@
-#!/usr/bin/env python3
-"""
-Detailed validation script for copier-config.yaml files
-"""
-
-import sys
-import yaml
-import re
-
-def validate_config(file_path):
-    """Validate a copier-config.yaml file and report all issues"""
-    
-    issues = []
-    warnings = []
-    
-    # Try to load the YAML
-    try:
-        with open(file_path, 'r') as f:
-            config = yaml.safe_load(f)
-    except yaml.YAMLError as e:
-        print(f"❌ YAML Parsing Error:")
-        print(f"   {e}")
-        return False
-    except Exception as e:
-        print(f"❌ Error reading file: {e}")
-        return False
-    
-    print("✅ YAML syntax is valid")
-    print()
-    
-    # Validate structure
-    if not isinstance(config, dict):
-        issues.append("Config must be a dictionary")
-        return False
-    
-    # Check required fields
-    if 'source_repo' not in config:
-        issues.append("Missing required field: source_repo")
-    
-    if 'copy_rules' not in config:
-        issues.append("Missing required field: copy_rules")
-    
-    if issues:
-        print("❌ Structural Issues:")
-        for issue in issues:
-            print(f"   - {issue}")
-        return False
-    
-    print(f"📋 Config Summary:")
-    print(f"   Source: {config.get('source_repo')}")
-    print(f"   Branch: {config.get('source_branch', 'main')}")
-    print(f"   Rules: {len(config.get('copy_rules', []))}")
-    print()
-    
-    # Validate each rule
-    rules = config.get('copy_rules', [])
-    for i, rule in enumerate(rules, 1):
-        rule_name = rule.get('name', f'Rule {i}')
-        print(f"🔍 Validating Rule {i}: {rule_name}")
-        
-        # Check rule structure
-        if 'source_pattern' not in rule:
-            issues.append(f"Rule '{rule_name}': Missing source_pattern")
-            continue
-        
-        if 'targets' not in rule:
-            issues.append(f"Rule '{rule_name}': Missing targets")
-            continue
-        
-        # Validate source_pattern
-        pattern = rule['source_pattern']
-        if not isinstance(pattern, dict):
-            issues.append(f"Rule '{rule_name}': source_pattern must be a dictionary")
-            continue
-        
-        pattern_type = pattern.get('type')
-        pattern_str = pattern.get('pattern')
-        
-        if not pattern_type:
-            issues.append(f"Rule '{rule_name}': Missing pattern type")
-        elif pattern_type not in ['prefix', 'glob', 'regex']:
-            issues.append(f"Rule '{rule_name}': Invalid pattern type '{pattern_type}' (must be prefix, glob, or regex)")
-        
-        if not pattern_str:
-            issues.append(f"Rule '{rule_name}': Missing pattern string")
-        else:
-            # Check for type/pattern mismatch
-            has_regex_syntax = bool(re.search(r'\(\?P<\w+>', pattern_str))
-            
-            if pattern_type == 'prefix' and has_regex_syntax:
-                issues.append(f"Rule '{rule_name}': Pattern type is 'prefix' but pattern contains regex syntax '(?P<...>)'")
-                warnings.append(f"Rule '{rule_name}': Should use type: 'regex' instead of 'prefix'")
-            
-            # Validate regex patterns
-            if pattern_type == 'regex':
-                try:
-                    re.compile(pattern_str)
-                except re.error as e:
-                    issues.append(f"Rule '{rule_name}': Invalid regex pattern: {e}")
-        
-        # Validate targets
-        targets = rule.get('targets', [])
-        if not isinstance(targets, list):
-            issues.append(f"Rule '{rule_name}': targets must be a list")
-            continue
-        
-        if len(targets) == 0:
-            warnings.append(f"Rule '{rule_name}': No targets defined")
-        
-        for j, target in enumerate(targets, 1):
-            if not isinstance(target, dict):
-                issues.append(f"Rule '{rule_name}', Target {j}: Must be a dictionary")
-                continue
-            
-            # Check required target fields
-            if 'repo' not in target:
-                issues.append(f"Rule '{rule_name}', Target {j}: Missing 'repo' field")
-            
-            if 'branch' not in target:
-                warnings.append(f"Rule '{rule_name}', Target {j}: Missing 'branch' field (will use default)")
-            
-            if 'path_transform' not in target:
-                warnings.append(f"Rule '{rule_name}', Target {j}: Missing 'path_transform' field")
-            
-            # Validate commit_strategy
-            if 'commit_strategy' in target:
-                strategy = target['commit_strategy']
-                if not isinstance(strategy, dict):
-                    issues.append(f"Rule '{rule_name}', Target {j}: commit_strategy must be a dictionary")
-                else:
-                    strategy_type = strategy.get('type')
-                    if strategy_type and strategy_type not in ['direct', 'pull_request']:
-                        issues.append(f"Rule '{rule_name}', Target {j}: Invalid commit_strategy type '{strategy_type}'")
-        
-        print(f"   ✓ Rule validated")
-    
-    print()
-    
-    # Print summary
-    if issues:
-        print("❌ VALIDATION FAILED")
-        print()
-        print("Issues found:")
-        for issue in issues:
-            print(f"   ❌ {issue}")
-        print()
-    
-    if warnings:
-        print("⚠️  Warnings:")
-        for warning in warnings:
-            print(f"   ⚠️  {warning}")
-        print()
-    
-    if not issues and not warnings:
-        print("✅ Configuration is valid with no issues!")
-        return True
-    elif not issues:
-        print("✅ Configuration is valid (with warnings)")
-        return True
-    else:
-        return False
-
-if __name__ == '__main__':
-    if len(sys.argv) != 2:
-        print("Usage: validate-config-detailed.py <config-file>")
-        sys.exit(1)
-    
-    file_path = sys.argv[1]
-    success = validate_config(file_path)
-    sys.exit(0 if success else 1)
-
diff --git a/services/audit_logger.go b/services/audit_logger.go
index b40a62c..7fa6fca 100644
--- a/services/audit_logger.go
+++ b/services/audit_logger.go
@@ -5,9 +5,9 @@ import (
 	"fmt"
 	"time"
 
-	"go.mongodb.org/mongo-driver/bson"
-	"go.mongodb.org/mongo-driver/mongo"
-	"go.mongodb.org/mongo-driver/mongo/options"
+	"go.mongodb.org/mongo-driver/v2/bson"
+	"go.mongodb.org/mongo-driver/v2/mongo"
+	"go.mongodb.org/mongo-driver/v2/mongo/options"
 )
 
 // AuditEventType represents the type of audit event
@@ -21,21 +21,21 @@ const (
 
 // AuditEvent represents an audit log entry
 type AuditEvent struct {
-	ID               string         `bson:"_id,omitempty"`
-	Timestamp        time.Time      `bson:"timestamp"`
-	EventType        AuditEventType `bson:"event_type"`
-	RuleName         string         `bson:"rule_name,omitempty"`
-	SourceRepo       string         `bson:"source_repo"`
-	SourcePath       string         `bson:"source_path"`
-	TargetRepo       string         `bson:"target_repo,omitempty"`
-	TargetPath       string         `bson:"target_path,omitempty"`
-	CommitSHA        string         `bson:"commit_sha,omitempty"`
-	PRNumber         int            `bson:"pr_number,omitempty"`
-	Success          bool           `bson:"success"`
-	ErrorMessage     string         `bson:"error_message,omitempty"`
-	DurationMs       int64          `bson:"duration_ms,omitempty"`
-	FileSize         int64          `bson:"file_size,omitempty"`
-	AdditionalData   map[string]any `bson:"additional_data,omitempty"`
+	ID             string         `bson:"_id,omitempty"`
+	Timestamp      time.Time      `bson:"timestamp"`
+	EventType      AuditEventType `bson:"event_type"`
+	RuleName       string         `bson:"rule_name,omitempty"`
+	SourceRepo     string         `bson:"source_repo"`
+	SourcePath     string         `bson:"source_path"`
+	TargetRepo     string         `bson:"target_repo,omitempty"`
+	TargetPath     string         `bson:"target_path,omitempty"`
+	CommitSHA      string         `bson:"commit_sha,omitempty"`
+	PRNumber       int            `bson:"pr_number,omitempty"`
+	Success        bool           `bson:"success"`
+	ErrorMessage   string         `bson:"error_message,omitempty"`
+	DurationMs     int64          `bson:"duration_ms,omitempty"`
+	FileSize       int64          `bson:"file_size,omitempty"`
+	AdditionalData map[string]any `bson:"additional_data,omitempty"`
 }
 
 // AuditLogger handles audit logging to MongoDB
@@ -48,24 +48,25 @@ type AuditLogger interface {
 	GetEventsByRule(ctx context.Context, ruleName string, limit int) ([]AuditEvent, error)
 	GetStatsByRule(ctx context.Context) (map[string]RuleStats, error)
 	GetDailyVolume(ctx context.Context, days int) ([]DailyStats, error)
+	Ping(ctx context.Context) error
 	Close(ctx context.Context) error
 }
 
 // RuleStats represents statistics for a specific rule
 type RuleStats struct {
-	RuleName     string `bson:"_id"`
-	TotalCopies  int    `bson:"total_copies"`
-	SuccessCount int    `bson:"success_count"`
-	FailureCount int    `bson:"failure_count"`
+	RuleName     string  `bson:"_id"`
+	TotalCopies  int     `bson:"total_copies"`
+	SuccessCount int     `bson:"success_count"`
+	FailureCount int     `bson:"failure_count"`
 	AvgDuration  float64 `bson:"avg_duration"`
 }
 
 // DailyStats represents daily copy volume statistics
 type DailyStats struct {
-	Date       string `bson:"_id"`
-	TotalCopies int   `bson:"total_copies"`
-	SuccessCount int  `bson:"success_count"`
-	FailureCount int  `bson:"failure_count"`
+	Date         string `bson:"_id"`
+	TotalCopies  int    `bson:"total_copies"`
+	SuccessCount int    `bson:"success_count"`
+	FailureCount int    `bson:"failure_count"`
 }
 
 // MongoAuditLogger implements AuditLogger using MongoDB
@@ -85,8 +86,14 @@ func NewMongoAuditLogger(ctx context.Context, mongoURI, database, collection str
 		return nil, fmt.Errorf("MONGO_URI is required when audit logging is enabled")
 	}
 
-	clientOptions := options.Client().ApplyURI(mongoURI)
-	client, err := mongo.Connect(ctx, clientOptions)
+	clientOptions := options.Client().
+		ApplyURI(mongoURI).
+		SetServerSelectionTimeout(5 * time.Second).
+		SetConnectTimeout(5 * time.Second).
+		SetTimeout(10 * time.Second).
+		SetMaxPoolSize(10).
+		SetRetryWrites(true)
+	client, err := mongo.Connect(clientOptions)
 	if err != nil {
 		return nil, fmt.Errorf("failed to connect to MongoDB: %w", err)
 	}
@@ -168,7 +175,7 @@ func (mal *MongoAuditLogger) GetRecentEvents(ctx context.Context, limit int) ([]
 	if err != nil {
 		return nil, err
 	}
-	defer cursor.Close(ctx)
+	defer func() { _ = cursor.Close(ctx) }()
 
 	var events []AuditEvent
 	if err := cursor.All(ctx, &events); err != nil {
@@ -185,7 +192,7 @@ func (mal *MongoAuditLogger) GetFailedEvents(ctx context.Context, limit int) ([]
 	if err != nil {
 		return nil, err
 	}
-	defer cursor.Close(ctx)
+	defer func() { _ = cursor.Close(ctx) }()
 
 	var events []AuditEvent
 	if err := cursor.All(ctx, &events); err != nil {
@@ -202,7 +209,7 @@ func (mal *MongoAuditLogger) GetEventsByRule(ctx context.Context, ruleName strin
 	if err != nil {
 		return nil, err
 	}
-	defer cursor.Close(ctx)
+	defer func() { _ = cursor.Close(ctx) }()
 
 	var events []AuditEvent
 	if err := cursor.All(ctx, &events); err != nil {
@@ -228,7 +235,7 @@ func (mal *MongoAuditLogger) GetStatsByRule(ctx context.Context) (map[string]Rul
 	if err != nil {
 		return nil, err
 	}
-	defer cursor.Close(ctx)
+	defer func() { _ = cursor.Close(ctx) }()
 
 	var stats []RuleStats
 	if err := cursor.All(ctx, &stats); err != nil {
@@ -245,7 +252,7 @@ func (mal *MongoAuditLogger) GetStatsByRule(ctx context.Context) (map[string]Rul
 // GetDailyVolume retrieves daily copy volume statistics
 func (mal *MongoAuditLogger) GetDailyVolume(ctx context.Context, days int) ([]DailyStats, error) {
 	startDate := time.Now().AddDate(0, 0, -days)
-	
+
 	pipeline := mongo.Pipeline{
 		{{Key: "$match", Value: bson.M{
 			"event_type": AuditEventCopy,
@@ -269,7 +276,7 @@ func (mal *MongoAuditLogger) GetDailyVolume(ctx context.Context, days int) ([]Da
 	if err != nil {
 		return nil, err
 	}
-	defer cursor.Close(ctx)
+	defer func() { _ = cursor.Close(ctx) }()
 
 	var stats []DailyStats
 	if err := cursor.All(ctx, &stats); err != nil {
@@ -278,7 +285,12 @@ func (mal *MongoAuditLogger) GetDailyVolume(ctx context.Context, days int) ([]Da
 	return stats, nil
 }
 
-// Close closes the MongoDB connection
+// Ping checks MongoDB connectivity.
+func (mal *MongoAuditLogger) Ping(ctx context.Context) error {
+	return mal.client.Ping(ctx, nil)
+}
+
+// Close closes the MongoDB connection.
 func (mal *MongoAuditLogger) Close(ctx context.Context) error {
 	return mal.client.Disconnect(ctx)
 }
@@ -286,9 +298,11 @@ func (mal *MongoAuditLogger) Close(ctx context.Context) error {
 // NoOpAuditLogger is a no-op implementation when audit logging is disabled
 type NoOpAuditLogger struct{}
 
-func (nal *NoOpAuditLogger) LogCopyEvent(ctx context.Context, event *AuditEvent) error        { return nil }
-func (nal *NoOpAuditLogger) LogDeprecationEvent(ctx context.Context, event *AuditEvent) error { return nil }
-func (nal *NoOpAuditLogger) LogErrorEvent(ctx context.Context, event *AuditEvent) error       { return nil }
+func (nal *NoOpAuditLogger) LogCopyEvent(ctx context.Context, event *AuditEvent) error { return nil }
+func (nal *NoOpAuditLogger) LogDeprecationEvent(ctx context.Context, event *AuditEvent) error {
+	return nil
+}
+func (nal *NoOpAuditLogger) LogErrorEvent(ctx context.Context, event *AuditEvent) error { return nil }
 func (nal *NoOpAuditLogger) GetRecentEvents(ctx context.Context, limit int) ([]AuditEvent, error) {
 	return []AuditEvent{}, nil
 }
@@ -304,5 +318,5 @@ func (nal *NoOpAuditLogger) GetStatsByRule(ctx context.Context) (map[string]Rule
 func (nal *NoOpAuditLogger) GetDailyVolume(ctx context.Context, days int) ([]DailyStats, error) {
 	return []DailyStats{}, nil
 }
+func (nal *NoOpAuditLogger) Ping(ctx context.Context) error  { return nil }
 func (nal *NoOpAuditLogger) Close(ctx context.Context) error { return nil }
-
diff --git a/services/config_loader.go b/services/config_loader.go
index f3567dd..185e4dc 100644
--- a/services/config_loader.go
+++ b/services/config_loader.go
@@ -4,8 +4,9 @@ import (
 	"context"
 	"fmt"
 	"os"
+	"strings"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"gopkg.in/yaml.v3"
 
 	"github.com/grove-platform/github-copier/configs"
@@ -51,14 +52,14 @@ func (cl *DefaultConfigLoader) LoadConfig(ctx context.Context, config *configs.C
 // LoadConfigFromContent loads configuration from a string
 func (cl *DefaultConfigLoader) LoadConfigFromContent(content string, filename string) (*types.YAMLConfig, error) {
 	if content == "" {
-		return nil, fmt.Errorf("config file is empty")
+		return nil, fmt.Errorf("%w: config file is empty", ErrConfigLoad)
 	}
 
 	// Parse as YAML (supports both YAML and JSON since YAML is a superset of JSON)
 	var yamlConfig types.YAMLConfig
 	err := yaml.Unmarshal([]byte(content), &yamlConfig)
 	if err != nil {
-		return nil, fmt.Errorf("failed to parse config file: %w", err)
+		return nil, fmt.Errorf("%w: failed to parse config file: %v", ErrConfigLoad, err)
 	}
 
 	// Set defaults
@@ -66,7 +67,7 @@ func (cl *DefaultConfigLoader) LoadConfigFromContent(content string, filename st
 
 	// Validate
 	if err := yamlConfig.Validate(); err != nil {
-		return nil, fmt.Errorf("config validation failed: %w", err)
+		return nil, fmt.Errorf("%w: %v", ErrConfigValidation, err)
 	}
 
 	return &yamlConfig, nil
@@ -75,7 +76,7 @@ func (cl *DefaultConfigLoader) LoadConfigFromContent(content string, filename st
 // retrieveConfigFileContent fetches the config file content from the repository
 func retrieveConfigFileContent(ctx context.Context, filePath string, config *configs.Config) (string, error) {
 	// Get GitHub client for the config repo's org (auto-discovers installation ID)
-	client, err := GetRestClientForOrg(config.ConfigRepoOwner)
+	client, err := GetRestClientForOrg(ctx, config, config.ConfigRepoOwner)
 	if err != nil {
 		return "", fmt.Errorf("failed to get GitHub client for org %s: %w", config.ConfigRepoOwner, err)
 	}
@@ -91,10 +92,15 @@ func retrieveConfigFileContent(ctx context.Context, filePath string, config *con
 		},
 	)
 	if err != nil {
+		// Check if this is an authentication error
+		errStr := err.Error()
+		if strings.Contains(errStr, "401") || strings.Contains(errStr, "Bad credentials") {
+			return "", fmt.Errorf("%w: unable to fetch config file. The GitHub App private key (PEM) may be invalid or expired. Please check the CODE_COPIER_PEM secret in GCP Secret Manager. Original error: %v", ErrAuthentication, err)
+		}
 		return "", fmt.Errorf("failed to get config file: %w", err)
 	}
 	if fileContent == nil {
-		return "", fmt.Errorf("config file content is nil for path: %s", filePath)
+		return "", fmt.Errorf("%w: config file at path: %s", ErrContentNil, filePath)
 	}
 
 	// Decode content
@@ -153,7 +159,7 @@ func (cv *ConfigValidator) TestTransform(sourcePath string, template string, var
 // This is useful for local testing and development
 func loadLocalConfigFile(filename string) (string, error) {
 	// Try to read from current directory
-	data, err := os.ReadFile(filename)
+	data, err := os.ReadFile(filename) // #nosec G304 -- local dev config path from caller
 	if err != nil {
 		return "", err
 	}
diff --git a/services/delivery_tracker.go b/services/delivery_tracker.go
new file mode 100644
index 0000000..fe36de0
--- /dev/null
+++ b/services/delivery_tracker.go
@@ -0,0 +1,90 @@
+package services
+
+import (
+	"sync"
+	"time"
+)
+
+// DeliveryTracker tracks processed GitHub webhook delivery IDs to prevent
+// duplicate processing. GitHub retries deliveries on timeout or error, and
+// the X-GitHub-Delivery header uniquely identifies each delivery.
+//
+// This is an in-memory implementation suitable for single-instance deployments.
+// For multi-instance deployments, replace with a shared store (e.g. MongoDB or Redis).
+type DeliveryTracker struct {
+	mu      sync.Mutex
+	entries map[string]time.Time
+	ttl     time.Duration
+
+	// stopCleanup signals the background goroutine to stop
+	stopCleanup chan struct{}
+}
+
+// NewDeliveryTracker creates a tracker that expires entries after the given TTL.
+// A background goroutine periodically purges expired entries.
+func NewDeliveryTracker(ttl time.Duration) *DeliveryTracker {
+	dt := &DeliveryTracker{
+		entries:     make(map[string]time.Time),
+		ttl:         ttl,
+		stopCleanup: make(chan struct{}),
+	}
+	go dt.cleanupLoop()
+	return dt
+}
+
+// TryRecord attempts to record a delivery ID. Returns true if the ID is new
+// (not a duplicate), false if it was already seen within the TTL window.
+func (dt *DeliveryTracker) TryRecord(deliveryID string) bool {
+	dt.mu.Lock()
+	defer dt.mu.Unlock()
+
+	if seenAt, exists := dt.entries[deliveryID]; exists {
+		if time.Since(seenAt) < dt.ttl {
+			return false // duplicate within TTL
+		}
+		// Expired entry — allow reprocessing
+	}
+
+	dt.entries[deliveryID] = time.Now()
+	return true
+}
+
+// Len returns the current number of tracked delivery IDs (for diagnostics).
+func (dt *DeliveryTracker) Len() int {
+	dt.mu.Lock()
+	defer dt.mu.Unlock()
+	return len(dt.entries)
+}
+
+// Stop halts the background cleanup goroutine.
+func (dt *DeliveryTracker) Stop() {
+	close(dt.stopCleanup)
+}
+
+// cleanupLoop periodically removes expired entries to bound memory usage.
+func (dt *DeliveryTracker) cleanupLoop() {
+	ticker := time.NewTicker(dt.ttl / 2)
+	defer ticker.Stop()
+
+	for {
+		select {
+		case <-ticker.C:
+			dt.purgeExpired()
+		case <-dt.stopCleanup:
+			return
+		}
+	}
+}
+
+// purgeExpired removes all entries older than TTL.
+func (dt *DeliveryTracker) purgeExpired() {
+	dt.mu.Lock()
+	defer dt.mu.Unlock()
+
+	now := time.Now()
+	for id, seenAt := range dt.entries {
+		if now.Sub(seenAt) >= dt.ttl {
+			delete(dt.entries, id)
+		}
+	}
+}
diff --git a/services/delivery_tracker_test.go b/services/delivery_tracker_test.go
new file mode 100644
index 0000000..0ebb725
--- /dev/null
+++ b/services/delivery_tracker_test.go
@@ -0,0 +1,137 @@
+package services
+
+import (
+	"fmt"
+	"sync"
+	"testing"
+	"time"
+)
+
+func TestDeliveryTracker_TryRecord(t *testing.T) {
+	dt := NewDeliveryTracker(1 * time.Hour)
+	defer dt.Stop()
+
+	// First call should succeed
+	if !dt.TryRecord("delivery-1") {
+		t.Error("expected first TryRecord to return true")
+	}
+
+	// Duplicate should be rejected
+	if dt.TryRecord("delivery-1") {
+		t.Error("expected duplicate TryRecord to return false")
+	}
+
+	// Different ID should succeed
+	if !dt.TryRecord("delivery-2") {
+		t.Error("expected TryRecord for new ID to return true")
+	}
+}
+
+func TestDeliveryTracker_TTLExpiry(t *testing.T) {
+	dt := NewDeliveryTracker(50 * time.Millisecond)
+	defer dt.Stop()
+
+	if !dt.TryRecord("delivery-1") {
+		t.Error("expected first TryRecord to return true")
+	}
+
+	// Wait for TTL to expire
+	time.Sleep(60 * time.Millisecond)
+
+	// Should allow reprocessing after expiry
+	if !dt.TryRecord("delivery-1") {
+		t.Error("expected TryRecord to return true after TTL expiry")
+	}
+}
+
+func TestDeliveryTracker_Len(t *testing.T) {
+	dt := NewDeliveryTracker(1 * time.Hour)
+	defer dt.Stop()
+
+	if dt.Len() != 0 {
+		t.Errorf("expected Len()=0, got %d", dt.Len())
+	}
+
+	dt.TryRecord("a")
+	dt.TryRecord("b")
+	dt.TryRecord("c")
+	dt.TryRecord("a") // duplicate, should not increase count
+
+	if dt.Len() != 3 {
+		t.Errorf("expected Len()=3, got %d", dt.Len())
+	}
+}
+
+func TestDeliveryTracker_PurgeExpired(t *testing.T) {
+	dt := NewDeliveryTracker(50 * time.Millisecond)
+	defer dt.Stop()
+
+	dt.TryRecord("a")
+	dt.TryRecord("b")
+
+	if dt.Len() != 2 {
+		t.Errorf("expected Len()=2, got %d", dt.Len())
+	}
+
+	// Wait for expiry + cleanup cycle (ttl/2 = 25ms, so total ~75ms should trigger)
+	time.Sleep(100 * time.Millisecond)
+
+	if dt.Len() != 0 {
+		t.Errorf("expected Len()=0 after purge, got %d", dt.Len())
+	}
+}
+
+func TestDeliveryTracker_ConcurrentAccess(t *testing.T) {
+	dt := NewDeliveryTracker(1 * time.Hour)
+	defer dt.Stop()
+
+	const goroutines = 50
+	var wg sync.WaitGroup
+	results := make([]bool, goroutines)
+
+	// All goroutines try to record the same delivery ID
+	wg.Add(goroutines)
+	for i := 0; i < goroutines; i++ {
+		go func(idx int) {
+			defer wg.Done()
+			results[idx] = dt.TryRecord("same-delivery")
+		}(i)
+	}
+	wg.Wait()
+
+	// Exactly one goroutine should succeed
+	successCount := 0
+	for _, ok := range results {
+		if ok {
+			successCount++
+		}
+	}
+	if successCount != 1 {
+		t.Errorf("expected exactly 1 success, got %d", successCount)
+	}
+}
+
+func TestDeliveryTracker_ConcurrentDifferentIDs(t *testing.T) {
+	dt := NewDeliveryTracker(1 * time.Hour)
+	defer dt.Stop()
+
+	const goroutines = 100
+	var wg sync.WaitGroup
+
+	// Each goroutine records a unique ID
+	wg.Add(goroutines)
+	for i := 0; i < goroutines; i++ {
+		go func(idx int) {
+			defer wg.Done()
+			id := fmt.Sprintf("delivery-%d", idx)
+			if !dt.TryRecord(id) {
+				t.Errorf("expected TryRecord(%s) to return true", id)
+			}
+		}(i)
+	}
+	wg.Wait()
+
+	if dt.Len() != goroutines {
+		t.Errorf("expected Len()=%d, got %d", goroutines, dt.Len())
+	}
+}
diff --git a/services/errors.go b/services/errors.go
new file mode 100644
index 0000000..5fc4f3d
--- /dev/null
+++ b/services/errors.go
@@ -0,0 +1,33 @@
+package services
+
+import "errors"
+
+// Sentinel errors for common failure modes. Wrap these with fmt.Errorf("%w", ...)
+// so callers can use errors.Is() to detect specific failure categories.
+var (
+	// ErrAuthentication indicates a GitHub App authentication failure
+	// (invalid PEM, expired key, bad JWT, etc.).
+	ErrAuthentication = errors.New("github app authentication failed")
+
+	// ErrSecretAccess indicates a failure to retrieve a secret from
+	// GCP Secret Manager or from the local environment fallback.
+	ErrSecretAccess = errors.New("secret access failed")
+
+	// ErrConfigLoad indicates a failure to load or parse the YAML configuration file.
+	ErrConfigLoad = errors.New("config load failed")
+
+	// ErrConfigValidation indicates the configuration was loaded but failed validation.
+	ErrConfigValidation = errors.New("config validation failed")
+
+	// ErrContentNil indicates that the GitHub API returned a nil content body
+	// for a file that was expected to exist.
+	ErrContentNil = errors.New("file content is nil")
+
+	// ErrInstallationNotFound indicates that no GitHub App installation was found
+	// for the given organization.
+	ErrInstallationNotFound = errors.New("no installation found for organization")
+
+	// ErrMergeConflict indicates a PR or ref update could not be completed
+	// due to merge conflicts or non-fast-forward push.
+	ErrMergeConflict = errors.New("merge conflict")
+)
diff --git a/services/file_state_service_test.go b/services/file_state_service_test.go
index 39bb2d9..92cd8bf 100644
--- a/services/file_state_service_test.go
+++ b/services/file_state_service_test.go
@@ -4,7 +4,7 @@ import (
 	"sync"
 	"testing"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/services"
 	"github.com/grove-platform/github-copier/types"
 	"github.com/stretchr/testify/assert"
@@ -26,7 +26,7 @@ func TestFileStateService_AddAndGetFilesToUpload(t *testing.T) {
 		CommitStrategy: types.CommitStrategyDirect,
 		CommitMessage:  "Test commit",
 		Content: []github.RepositoryContent{
-			{Path: github.String("test.go")},
+			{Path: github.Ptr("test.go")},
 		},
 	}
 
@@ -193,7 +193,7 @@ func TestFileStateService_UpdateExistingFile(t *testing.T) {
 	content1 := types.UploadFileContent{
 		TargetBranch: "main",
 		Content: []github.RepositoryContent{
-			{Path: github.String("file1.go")},
+			{Path: github.Ptr("file1.go")},
 		},
 	}
 	service.AddFileToUpload(key, content1)
@@ -202,8 +202,8 @@ func TestFileStateService_UpdateExistingFile(t *testing.T) {
 	content2 := types.UploadFileContent{
 		TargetBranch: "main",
 		Content: []github.RepositoryContent{
-			{Path: github.String("file1.go")},
-			{Path: github.String("file2.go")},
+			{Path: github.Ptr("file1.go")},
+			{Path: github.Ptr("file2.go")},
 		},
 	}
 	service.AddFileToUpload(key, content2)
@@ -271,14 +271,14 @@ func TestFileStateService_MultipleRepos(t *testing.T) {
 	content1 := types.UploadFileContent{
 		TargetBranch: "main",
 		Content: []github.RepositoryContent{
-			{Path: github.String("file1.go")},
+			{Path: github.Ptr("file1.go")},
 		},
 	}
 
 	content2 := types.UploadFileContent{
 		TargetBranch: "develop",
 		Content: []github.RepositoryContent{
-			{Path: github.String("file2.go")},
+			{Path: github.Ptr("file2.go")},
 		},
 	}
 
@@ -305,7 +305,7 @@ func TestFileStateService_IsolatedCopies(t *testing.T) {
 	content := types.UploadFileContent{
 		TargetBranch: "main",
 		Content: []github.RepositoryContent{
-			{Path: github.String("file1.go")},
+			{Path: github.Ptr("file1.go")},
 		},
 	}
 
diff --git a/services/github_auth.go b/services/github_auth.go
index 683463f..77bd95b 100644
--- a/services/github_auth.go
+++ b/services/github_auth.go
@@ -14,7 +14,7 @@ import (
 	secretmanager "cloud.google.com/go/secretmanager/apiv1"
 	"cloud.google.com/go/secretmanager/apiv1/secretmanagerpb"
 	"github.com/golang-jwt/jwt/v5"
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/configs"
 	"github.com/shurcooL/graphql"
 	"golang.org/x/oauth2"
@@ -25,28 +25,11 @@ type transport struct {
 	token string
 }
 
-var InstallationAccessToken string
-var HTTPClient = http.DefaultClient
-
-// installationTokenCache caches installation access tokens by organization name
-var installationTokenCache = make(map[string]string)
-
-// jwtToken caches the GitHub App JWT token
-var jwtToken string
-var jwtExpiry time.Time
-
 // ConfigurePermissions sets up the necessary permissions to interact with the GitHub API.
 // It retrieves the GitHub App's private key from Google Secret Manager, generates a JWT,
-// and exchanges it for an installation access token.
-func ConfigurePermissions() error {
-	envFilePath := os.Getenv("ENV_FILE")
-
-	_, err := configs.LoadEnvironment(envFilePath)
-	if err != nil {
-		return fmt.Errorf("failed to load environment: %w", err)
-	}
-
-	pemKey, err := getPrivateKeyFromSecret()
+// and exchanges it for an installation access token stored in the TokenManager.
+func ConfigurePermissions(ctx context.Context, config *configs.Config) error {
+	pemKey, err := getPrivateKeyFromSecret(ctx, config)
 	if err != nil {
 		return fmt.Errorf("failed to get private key: %w", err)
 	}
@@ -57,30 +40,29 @@ func ConfigurePermissions() error {
 	}
 
 	// Generate JWT — use the numeric GitHub App ID (GITHUB_APP_ID) as "iss"
-	token, err := generateGitHubJWT(os.Getenv(configs.AppId), privateKey)
+	token, err := generateGitHubJWT(config.AppId, privateKey)
 	if err != nil {
 		return fmt.Errorf("error generating JWT: %w", err)
 	}
 
-	installationToken, err := getInstallationAccessToken("", token, HTTPClient)
+	hc := defaultTokenManager.GetHTTPClient()
+	installationToken, _, err := getInstallationAccessToken(config.InstallationId, token, hc)
 	if err != nil {
 		return fmt.Errorf("error getting installation access token: %w", err)
 	}
-	InstallationAccessToken = installationToken
+	defaultTokenManager.SetInstallationAccessToken(installationToken)
 	return nil
 }
 
 // generateGitHubJWT creates a JWT for GitHub App authentication.
 func generateGitHubJWT(appID string, privateKey *rsa.PrivateKey) (string, error) {
-	// Create a new JWT token
 	now := time.Now()
 	claims := jwt.MapClaims{
-		"iat": now.Unix(),                       // Issued at
-		"exp": now.Add(time.Minute * 10).Unix(), // Expiration time, 10 minutes from issue
-		"iss": appID,                            // GitHub App ID
+		"iat": now.Unix(),
+		"exp": now.Add(time.Minute * 10).Unix(),
+		"iss": appID,
 	}
 	token := jwt.NewWithClaims(jwt.SigningMethodRS256, claims)
-	// Sign the JWT with the private key
 	signedToken, err := token.SignedString(privateKey)
 	if err != nil {
 		return "", fmt.Errorf("unable to sign JWT: %v", err)
@@ -90,8 +72,8 @@ func generateGitHubJWT(appID string, privateKey *rsa.PrivateKey) (string, error)
 
 // getPrivateKeyFromSecret retrieves the GitHub App's private key from Google Secret Manager.
 // It supports local testing by allowing the key to be provided via environment variables.
-func getPrivateKeyFromSecret() ([]byte, error) {
-	if os.Getenv("SKIP_SECRET_MANAGER") == "true" { // for tests and local runs
+func getPrivateKeyFromSecret(ctx context.Context, config *configs.Config) ([]byte, error) {
+	if os.Getenv("SKIP_SECRET_MANAGER") == "true" {
 		if pem := os.Getenv("GITHUB_APP_PRIVATE_KEY"); pem != "" {
 			return []byte(pem), nil
 		}
@@ -102,67 +84,56 @@ func getPrivateKeyFromSecret() ([]byte, error) {
 			}
 			return dec, nil
 		}
-		return nil, fmt.Errorf("SKIP_SECRET_MANAGER=true but no GITHUB_APP_PRIVATE_KEY or GITHUB_APP_PRIVATE_KEY_B64 set")
+		return nil, fmt.Errorf("%w: SKIP_SECRET_MANAGER=true but no GITHUB_APP_PRIVATE_KEY or GITHUB_APP_PRIVATE_KEY_B64 set", ErrSecretAccess)
 	}
-	ctx := context.Background()
 	client, err := secretmanager.NewClient(ctx)
-
 	if err != nil {
-		return nil, fmt.Errorf("failed to create Secret Manager client: %w", err)
-	}
-	defer client.Close()
-
-	secretName := os.Getenv(configs.PEMKeyName)
-	if secretName == "" {
-		secretName = configs.NewConfig().PEMKeyName
+		return nil, fmt.Errorf("%w: failed to create Secret Manager client: %v", ErrSecretAccess, err)
 	}
+	defer func() { _ = client.Close() }()
 
 	req := &secretmanagerpb.AccessSecretVersionRequest{
-		Name: secretName,
+		Name: config.SecretPath(config.PEMKeyName),
 	}
 	result, err := client.AccessSecretVersion(ctx, req)
 	if err != nil {
-		return nil, fmt.Errorf("failed to access secret version: %w", err)
+		return nil, fmt.Errorf("%w: %v", ErrSecretAccess, err)
 	}
 	return result.Payload.Data, nil
 }
 
 // getWebhookSecretFromSecretManager retrieves the webhook secret from Google Cloud Secret Manager
-func getWebhookSecretFromSecretManager(secretName string) (string, error) {
+func getWebhookSecretFromSecretManager(ctx context.Context, secretName string) (string, error) {
 	if os.Getenv("SKIP_SECRET_MANAGER") == "true" {
-		// For tests and local runs, use direct env var
 		if secret := os.Getenv(configs.WebhookSecret); secret != "" {
 			return secret, nil
 		}
-		return "", fmt.Errorf("SKIP_SECRET_MANAGER=true but no WEBHOOK_SECRET set")
+		return "", fmt.Errorf("%w: SKIP_SECRET_MANAGER=true but no WEBHOOK_SECRET set", ErrSecretAccess)
 	}
 
-	ctx := context.Background()
 	client, err := secretmanager.NewClient(ctx)
 	if err != nil {
-		return "", fmt.Errorf("failed to create Secret Manager client: %w", err)
+		return "", fmt.Errorf("%w: failed to create Secret Manager client: %v", ErrSecretAccess, err)
 	}
-	defer client.Close()
+	defer func() { _ = client.Close() }()
 
 	req := &secretmanagerpb.AccessSecretVersionRequest{
 		Name: secretName,
 	}
 	result, err := client.AccessSecretVersion(ctx, req)
 	if err != nil {
-		return "", fmt.Errorf("failed to access secret version: %w", err)
+		return "", fmt.Errorf("%w: %v", ErrSecretAccess, err)
 	}
 	return string(result.Payload.Data), nil
 }
 
 // LoadWebhookSecret loads the webhook secret from Secret Manager or environment variable
-func LoadWebhookSecret(config *configs.Config) error {
-	// If webhook secret is already set directly, use it
+func LoadWebhookSecret(ctx context.Context, config *configs.Config) error {
 	if config.WebhookSecret != "" {
 		return nil
 	}
-
-	// Otherwise, load from Secret Manager
-	secret, err := getWebhookSecretFromSecretManager(config.WebhookSecretName)
+	resolvedName := config.SecretPath(config.WebhookSecretName)
+	secret, err := getWebhookSecretFromSecretManager(ctx, resolvedName)
 	if err != nil {
 		return fmt.Errorf("failed to load webhook secret: %w", err)
 	}
@@ -171,19 +142,15 @@ func LoadWebhookSecret(config *configs.Config) error {
 }
 
 // LoadMongoURI loads the MongoDB URI from Secret Manager or environment variable
-func LoadMongoURI(config *configs.Config) error {
-	// If MongoDB URI is already set directly, use it
+func LoadMongoURI(ctx context.Context, config *configs.Config) error {
 	if config.MongoURI != "" {
 		return nil
 	}
-
-	// If no secret name is configured, skip (audit logging is optional)
 	if config.MongoURISecretName == "" {
 		return nil
 	}
-
-	// Load from Secret Manager
-	uri, err := getSecretFromSecretManager(config.MongoURISecretName, "MONGO_URI")
+	resolvedName := config.SecretPath(config.MongoURISecretName)
+	uri, err := getSecretFromSecretManager(ctx, resolvedName, "MONGO_URI")
 	if err != nil {
 		return fmt.Errorf("failed to load MongoDB URI: %w", err)
 	}
@@ -192,47 +159,43 @@ func LoadMongoURI(config *configs.Config) error {
 }
 
 // getSecretFromSecretManager is a generic function to retrieve any secret from Secret Manager
-func getSecretFromSecretManager(secretName, envVarName string) (string, error) {
+func getSecretFromSecretManager(ctx context.Context, secretName, envVarName string) (string, error) {
 	if os.Getenv("SKIP_SECRET_MANAGER") == "true" {
-		// For tests and local runs, use direct env var
 		if secret := os.Getenv(envVarName); secret != "" {
 			return secret, nil
 		}
-		return "", fmt.Errorf("SKIP_SECRET_MANAGER=true but no %s set", envVarName)
+		return "", fmt.Errorf("%w: SKIP_SECRET_MANAGER=true but no %s set", ErrSecretAccess, envVarName)
 	}
 
-	ctx := context.Background()
 	client, err := secretmanager.NewClient(ctx)
 	if err != nil {
-		return "", fmt.Errorf("failed to create Secret Manager client: %w", err)
+		return "", fmt.Errorf("%w: failed to create Secret Manager client: %v", ErrSecretAccess, err)
 	}
-	defer client.Close()
+	defer func() { _ = client.Close() }()
 
 	req := &secretmanagerpb.AccessSecretVersionRequest{
 		Name: secretName,
 	}
 	result, err := client.AccessSecretVersion(ctx, req)
 	if err != nil {
-		return "", fmt.Errorf("failed to access secret version: %w", err)
+		return "", fmt.Errorf("%w: %v", ErrSecretAccess, err)
 	}
 	return string(result.Payload.Data), nil
 }
 
 // getInstallationAccessToken exchanges a JWT for a GitHub App installation access token.
-func getInstallationAccessToken(installationId, jwtToken string, hc *http.Client) (string, error) {
-	if installationId == "" || installationId == configs.InstallationId {
-		installationId = os.Getenv(configs.InstallationId)
-	}
+// Returns the token, its expiry time, and any error.
+func getInstallationAccessToken(installationId, jwtTokenStr string, hc *http.Client) (string, time.Time, error) {
 	if installationId == "" {
-		return "", fmt.Errorf("missing installation ID")
+		return "", time.Time{}, fmt.Errorf("missing installation ID")
 	}
 
 	url := fmt.Sprintf("https://api.github.com/app/installations/%s/access_tokens", installationId)
 	req, err := http.NewRequest("POST", url, nil)
 	if err != nil {
-		return "", fmt.Errorf("create request: %w", err)
+		return "", time.Time{}, fmt.Errorf("create request: %w", err)
 	}
-	req.Header.Set("Authorization", "Bearer "+jwtToken)
+	req.Header.Set("Authorization", "Bearer "+jwtTokenStr)
 	req.Header.Set("Accept", "application/vnd.github+json")
 
 	if hc == nil {
@@ -240,62 +203,92 @@ func getInstallationAccessToken(installationId, jwtToken string, hc *http.Client
 	}
 	resp, err := hc.Do(req)
 	if err != nil {
-		return "", fmt.Errorf("execute request: %w", err)
+		return "", time.Time{}, fmt.Errorf("execute request: %w", err)
 	}
-	defer resp.Body.Close()
+	defer func() { _ = resp.Body.Close() }()
 
 	if resp.StatusCode != http.StatusCreated {
-		b, _ := io.ReadAll(resp.Body)
-		return "", fmt.Errorf("status %d: %s", resp.StatusCode, string(b))
+		b, readErr := io.ReadAll(resp.Body)
+		if readErr != nil {
+			b = []byte(fmt.Sprintf("<failed to read body: %v>", readErr))
+		}
+		if resp.StatusCode == http.StatusUnauthorized {
+			return "", time.Time{}, fmt.Errorf("%w: failed to get installation access token (401). The GitHub App private key (PEM) may be invalid or expired. Please check the CODE_COPIER_PEM secret in GCP Secret Manager. Response: %s", ErrAuthentication, string(b))
+		}
+		return "", time.Time{}, fmt.Errorf("%w: status %d: %s", ErrAuthentication, resp.StatusCode, string(b))
 	}
 	var out struct {
-		Token string `json:"token"`
+		Token     string    `json:"token"`
+		ExpiresAt time.Time `json:"expires_at"`
 	}
 	if err = json.NewDecoder(resp.Body).Decode(&out); err != nil {
-		return "", fmt.Errorf("decode: %w", err)
+		return "", time.Time{}, fmt.Errorf("decode: %w", err)
 	}
-	return out.Token, nil
+	return out.Token, out.ExpiresAt, nil
 }
 
-// GetRestClient returns a GitHub REST API client authenticated with the installation access token.
+// GetRestClient returns a GitHub REST API client authenticated with the default installation access token.
 func GetRestClient() *github.Client {
-	src := oauth2.StaticTokenSource(&oauth2.Token{AccessToken: InstallationAccessToken})
+	tm := defaultTokenManager
+	token := tm.GetInstallationAccessToken()
+	hc := tm.GetHTTPClient()
+	return newGitHubRESTClient(token, hc)
+}
 
-	base := http.DefaultTransport
-	if HTTPClient != nil && HTTPClient.Transport != nil {
-		base = HTTPClient.Transport
+// GetGraphQLClient returns a GitHub GraphQL API client authenticated with the default installation access token.
+func GetGraphQLClient(ctx context.Context, config *configs.Config) (*graphql.Client, error) {
+	if defaultTokenManager.GetInstallationAccessToken() == "" {
+		if err := ConfigurePermissions(ctx, config); err != nil {
+			return nil, fmt.Errorf("failed to configure permissions: %w", err)
+		}
 	}
+	client := graphql.NewClient("https://api.github.com/graphql", &http.Client{
+		Transport: newRateLimitTransport(&transport{token: defaultTokenManager.GetInstallationAccessToken()}, nil),
+	})
+	return client, nil
+}
 
-	httpClient := &http.Client{
-		Transport: &oauth2.Transport{
-			Source: src,
-			Base:   base,
-		},
+// GetGraphQLClientForOrg returns a GitHub GraphQL API client authenticated for a specific organization.
+// Uses the TokenManager for thread-safe token caching with expiry tracking.
+func GetGraphQLClientForOrg(ctx context.Context, config *configs.Config, org string) (*graphql.Client, error) {
+	if token, ok := defaultTokenManager.GetTokenForOrg(org); ok {
+		client := graphql.NewClient("https://api.github.com/graphql", &http.Client{
+			Transport: newRateLimitTransport(&transport{token: token}, nil),
+		})
+		return client, nil
 	}
-	return github.NewClient(httpClient)
-}
 
-func GetGraphQLClient() (*graphql.Client, error) {
-	if InstallationAccessToken == "" {
-		if err := ConfigurePermissions(); err != nil {
-			return nil, fmt.Errorf("failed to configure permissions: %w", err)
-		}
+	installationID, err := getInstallationIDForOrg(ctx, config, org)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get installation ID for org %s: %w", org, err)
+	}
+
+	token, err := getOrRefreshJWT(ctx, config)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get JWT: %w", err)
 	}
+
+	hc := defaultTokenManager.GetHTTPClient()
+	installationToken, expiresAt, err := getInstallationAccessToken(installationID, token, hc)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get installation token for org %s: %w", org, err)
+	}
+
+	defaultTokenManager.SetTokenForOrg(org, installationToken, expiresAt)
+
 	client := graphql.NewClient("https://api.github.com/graphql", &http.Client{
-		Transport: &transport{token: InstallationAccessToken},
+		Transport: newRateLimitTransport(&transport{token: installationToken}, nil),
 	})
 	return client, nil
 }
 
-// getOrRefreshJWT returns a valid JWT token, generating a new one if expired
-func getOrRefreshJWT() (string, error) {
-	// Check if we have a valid cached JWT
-	if jwtToken != "" && time.Now().Before(jwtExpiry) {
-		return jwtToken, nil
+// getOrRefreshJWT returns a valid JWT token, generating a new one if expired.
+func getOrRefreshJWT(ctx context.Context, config *configs.Config) (string, error) {
+	if cachedToken, ok := defaultTokenManager.GetCachedJWT(); ok {
+		return cachedToken, nil
 	}
 
-	// Generate new JWT
-	pemKey, err := getPrivateKeyFromSecret()
+	pemKey, err := getPrivateKeyFromSecret(ctx, config)
 	if err != nil {
 		return "", fmt.Errorf("failed to get private key: %w", err)
 	}
@@ -305,21 +298,18 @@ func getOrRefreshJWT() (string, error) {
 		return "", fmt.Errorf("unable to parse RSA private key: %w", err)
 	}
 
-	token, err := generateGitHubJWT(os.Getenv(configs.AppId), privateKey)
+	token, err := generateGitHubJWT(config.AppId, privateKey)
 	if err != nil {
 		return "", fmt.Errorf("error generating JWT: %w", err)
 	}
 
-	// Cache the JWT (expires in 10 minutes, cache for 9 to be safe)
-	jwtToken = token
-	jwtExpiry = time.Now().Add(9 * time.Minute)
-
+	defaultTokenManager.SetCachedJWT(token, time.Now().Add(9*time.Minute))
 	return token, nil
 }
 
 // getInstallationIDForOrg retrieves the installation ID for a specific organization
-func getInstallationIDForOrg(org string) (string, error) {
-	token, err := getOrRefreshJWT()
+func getInstallationIDForOrg(ctx context.Context, config *configs.Config, org string) (string, error) {
+	token, err := getOrRefreshJWT(ctx, config)
 	if err != nil {
 		return "", fmt.Errorf("failed to get JWT: %w", err)
 	}
@@ -332,20 +322,22 @@ func getInstallationIDForOrg(org string) (string, error) {
 	req.Header.Set("Authorization", "Bearer "+token)
 	req.Header.Set("Accept", "application/vnd.github+json")
 
-	hc := HTTPClient
-	if hc == nil {
-		hc = http.DefaultClient
-	}
-
+	hc := defaultTokenManager.GetHTTPClient()
 	resp, err := hc.Do(req)
 	if err != nil {
 		return "", fmt.Errorf("request failed: %w", err)
 	}
-	defer resp.Body.Close()
+	defer func() { _ = resp.Body.Close() }()
 
 	if resp.StatusCode != http.StatusOK {
-		body, _ := io.ReadAll(resp.Body)
-		return "", fmt.Errorf("GET %s: %d %s %s", url, resp.StatusCode, resp.Status, body)
+		body, readErr := io.ReadAll(resp.Body)
+		if readErr != nil {
+			body = []byte(fmt.Sprintf("<failed to read body: %v>", readErr))
+		}
+		if resp.StatusCode == http.StatusUnauthorized {
+			return "", fmt.Errorf("%w: the GitHub App private key (PEM) may be invalid or expired. Please check the CODE_COPIER_PEM secret in GCP Secret Manager. Response: %s", ErrAuthentication, string(body))
+		}
+		return "", fmt.Errorf("%w: GET %s: %d %s %s", ErrAuthentication, url, resp.StatusCode, resp.Status, body)
 	}
 
 	var installations []struct {
@@ -360,74 +352,65 @@ func getInstallationIDForOrg(org string) (string, error) {
 		return "", fmt.Errorf("decode response: %w", err)
 	}
 
-	// Find the installation for the specified organization
 	for _, inst := range installations {
 		if inst.Account.Login == org {
 			return fmt.Sprintf("%d", inst.ID), nil
 		}
 	}
 
-	return "", fmt.Errorf("no installation found for organization: %s", org)
+	return "", fmt.Errorf("%w: %s", ErrInstallationNotFound, org)
 }
 
 // SetInstallationTokenForOrg sets a cached installation token for an organization.
 // This is primarily used for testing to bypass the GitHub App authentication flow.
 func SetInstallationTokenForOrg(org, token string) {
-	installationTokenCache[org] = token
+	defaultTokenManager.SetTokenForOrgNoExpiry(org, token)
 }
 
-// GetRestClientForOrg returns a GitHub REST API client authenticated for a specific organization
-func GetRestClientForOrg(org string) (*github.Client, error) {
-	// Check if we have a cached token for this org
-	if token, ok := installationTokenCache[org]; ok && token != "" {
-		src := oauth2.StaticTokenSource(&oauth2.Token{AccessToken: token})
-		base := http.DefaultTransport
-		if HTTPClient != nil && HTTPClient.Transport != nil {
-			base = HTTPClient.Transport
-		}
-		httpClient := &http.Client{
-			Transport: &oauth2.Transport{
-				Source: src,
-				Base:   base,
-			},
-		}
-		return github.NewClient(httpClient), nil
+// GetRestClientForOrg returns a GitHub REST API client authenticated for a specific organization.
+func GetRestClientForOrg(ctx context.Context, config *configs.Config, org string) (*github.Client, error) {
+	tm := defaultTokenManager
+	hc := tm.GetHTTPClient()
+
+	if token, ok := tm.GetTokenForOrg(org); ok {
+		return newGitHubRESTClient(token, hc), nil
 	}
 
-	// Get installation ID for the organization
-	installationID, err := getInstallationIDForOrg(org)
+	installationID, err := getInstallationIDForOrg(ctx, config, org)
 	if err != nil {
 		return nil, fmt.Errorf("failed to get installation ID for org %s: %w", org, err)
 	}
 
-	// Get JWT token
-	token, err := getOrRefreshJWT()
+	token, err := getOrRefreshJWT(ctx, config)
 	if err != nil {
 		return nil, fmt.Errorf("failed to get JWT: %w", err)
 	}
 
-	// Get installation access token
-	installationToken, err := getInstallationAccessToken(installationID, token, HTTPClient)
+	installationToken, expiresAt, err := getInstallationAccessToken(installationID, token, hc)
 	if err != nil {
 		return nil, fmt.Errorf("failed to get installation token for org %s: %w", org, err)
 	}
 
-	// Cache the token
-	installationTokenCache[org] = installationToken
+	tm.SetTokenForOrg(org, installationToken, expiresAt)
+	return newGitHubRESTClient(installationToken, hc), nil
+}
 
-	// Create and return client
-	src := oauth2.StaticTokenSource(&oauth2.Token{AccessToken: installationToken})
+// newGitHubRESTClient creates a GitHub REST client with the given token and base HTTP client.
+// The transport chain is: rateLimitTransport → oauth2.Transport → base.
+func newGitHubRESTClient(token string, hc *http.Client) *github.Client {
+	src := oauth2.StaticTokenSource(&oauth2.Token{AccessToken: token})
 	base := http.DefaultTransport
-	if HTTPClient != nil && HTTPClient.Transport != nil {
-		base = HTTPClient.Transport
+	if hc != nil && hc.Transport != nil {
+		base = hc.Transport
+	}
+	oauthTransport := &oauth2.Transport{
+		Source: src,
+		Base:   base,
 	}
 	httpClient := &http.Client{
-		Transport: &oauth2.Transport{
-			Source: src,
-			Base:   base,
-		},
+		Transport: newRateLimitTransport(oauthTransport, nil),
 	}
-	return github.NewClient(httpClient), nil
+	return github.NewClient(httpClient)
 }
 
 // RoundTrip adds the Authorization header to each request.
diff --git a/services/github_auth_test.go b/services/github_auth_test.go
index cbb6f6c..ed40f31 100644
--- a/services/github_auth_test.go
+++ b/services/github_auth_test.go
@@ -1,116 +1,178 @@
 package services
 
 import (
+	"context"
+	"crypto/rand"
+	"crypto/rsa"
+	"crypto/x509"
+	"encoding/base64"
+	"encoding/pem"
+	"errors"
+	"net/http"
 	"os"
 	"testing"
 	"time"
 
+	"github.com/golang-jwt/jwt/v5"
 	"github.com/grove-platform/github-copier/configs"
+	"github.com/jarcoal/httpmock"
 )
 
-func TestGenerateGitHubJWT_EmptyAppID(t *testing.T) {
-	// Note: generateGitHubJWT requires appID string and *rsa.PrivateKey
-	// Testing this requires creating a valid RSA private key, which is complex
-	// This test documents the expected behavior
-	t.Skip("Skipping test that requires valid RSA private key generation")
+func TestGenerateGitHubJWT(t *testing.T) {
+	key, err := rsa.GenerateKey(rand.Reader, 2048)
+	if err != nil {
+		t.Fatalf("GenerateKey: %v", err)
+	}
+
+	tests := []struct {
+		name    string
+		appID   string
+		wantErr bool
+	}{
+		{name: "valid app ID", appID: "123456", wantErr: false},
+		{name: "empty app ID still produces JWT", appID: "", wantErr: false},
+	}
 
-	// Expected behavior:
-	// - Should return error with empty app ID
-	// - Should return error with nil private key
-	// - Should generate valid JWT with valid inputs
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			token, err := generateGitHubJWT(tt.appID, key)
+			if (err != nil) != tt.wantErr {
+				t.Fatalf("generateGitHubJWT() error = %v, wantErr %v", err, tt.wantErr)
+			}
+			if !tt.wantErr {
+				if token == "" {
+					t.Error("expected non-empty JWT token")
+				}
+				// Verify the token can be parsed and has correct claims
+				parsed, err := jwt.Parse(token, func(t *jwt.Token) (interface{}, error) {
+					return &key.PublicKey, nil
+				})
+				if err != nil {
+					t.Fatalf("jwt.Parse: %v", err)
+				}
+				claims, ok := parsed.Claims.(jwt.MapClaims)
+				if !ok {
+					t.Fatal("expected MapClaims")
+				}
+				if iss, _ := claims["iss"].(string); iss != tt.appID {
+					t.Errorf("iss = %q, want %q", iss, tt.appID)
+				}
+				if _, ok := claims["iat"]; !ok {
+					t.Error("missing 'iat' claim")
+				}
+				if _, ok := claims["exp"]; !ok {
+					t.Error("missing 'exp' claim")
+				}
+			}
+		})
+	}
 }
 
-func TestJWTCaching(t *testing.T) {
-	// Test JWT caching behavior
-	originalToken := jwtToken
-	originalExpiry := jwtExpiry
+func TestGenerateGitHubJWT_NilKey(t *testing.T) {
+	// The JWT library panics on nil key, so verify we get a panic.
 	defer func() {
-		jwtToken = originalToken
-		jwtExpiry = originalExpiry
+		if r := recover(); r == nil {
+			t.Error("expected panic with nil private key")
+		}
 	}()
+	_, _ = generateGitHubJWT("123456", nil)
+}
+
+func TestJWTCaching(t *testing.T) {
+	tm := NewTokenManager()
 
 	// Set a cached token that hasn't expired
-	jwtToken = "cached-token"
-	jwtExpiry = time.Now().Add(5 * time.Minute)
+	tm.SetCachedJWT("cached-token", time.Now().Add(5*time.Minute))
+
+	token, ok := tm.GetCachedJWT()
+	if !ok {
+		t.Error("Expected cached JWT to be valid")
+	}
+	if token != "cached-token" {
+		t.Errorf("Cached JWT = %s, want cached-token", token)
+	}
+
+	// Set an expired token
+	tm.SetCachedJWT("expired-token", time.Now().Add(-1*time.Minute))
 
-	// Note: getOrRefreshJWT is not exported, so we can't test it directly
-	// This test documents the expected caching behavior:
-	// - If jwtToken is set and jwtExpiry is in the future, return cached token
-	// - If jwtToken is empty or jwtExpiry is in the past, generate new token
-	// - Cache the new token and set expiry to 9 minutes from now
+	_, ok = tm.GetCachedJWT()
+	if ok {
+		t.Error("Expected expired JWT to not be returned")
+	}
 }
 
 func TestInstallationTokenCache_Structure(t *testing.T) {
-	// Test that we can manipulate the installation token cache
-	originalCache := installationTokenCache
-	defer func() {
-		installationTokenCache = originalCache
-	}()
+	tm := NewTokenManager()
 
-	// Initialize cache (it's a map[string]string)
-	installationTokenCache = make(map[string]string)
-
-	// Add a token
 	testToken := "test-token-value"
-	installationTokenCache["test-org"] = testToken
+	tm.SetTokenForOrgNoExpiry("test-org", testToken)
 
-	// Verify it was added
-	cached, exists := installationTokenCache["test-org"]
-	if !exists {
+	cached, ok := tm.GetTokenForOrg("test-org")
+	if !ok {
 		t.Error("Token not found in cache")
 	}
-
 	if cached != testToken {
 		t.Errorf("Cached token = %s, want %s", cached, testToken)
 	}
 }
 
-func TestLoadWebhookSecret_FromEnv(t *testing.T) {
-	// Test loading webhook secret from environment variable
-	testSecret := "test-webhook-secret"
-	os.Setenv("WEBHOOK_SECRET", testSecret)
-	defer os.Unsetenv("WEBHOOK_SECRET")
+func TestInstallationTokenCache_ExpiryTracking(t *testing.T) {
+	tm := NewTokenManager()
 
-	// LoadWebhookSecret requires a config parameter
-	config := &configs.Config{
-		WebhookSecret: "",
+	// Token with future expiry should be valid
+	tm.SetTokenForOrg("future-org", "valid-token", time.Now().Add(1*time.Hour))
+	token, ok := tm.GetTokenForOrg("future-org")
+	if !ok {
+		t.Error("Expected valid token to be returned")
 	}
+	if token != "valid-token" {
+		t.Errorf("Token = %s, want valid-token", token)
+	}
+
+	// Token within the 5-minute buffer should be treated as expired
+	tm.SetTokenForOrg("expiring-org", "expiring-token", time.Now().Add(3*time.Minute))
+	_, ok = tm.GetTokenForOrg("expiring-org")
+	if ok {
+		t.Error("Expected token within 5-minute buffer to not be returned")
+	}
+
+	// Already-expired token should not be returned
+	tm.SetTokenForOrg("expired-org", "expired-token", time.Now().Add(-10*time.Minute))
+	_, ok = tm.GetTokenForOrg("expired-org")
+	if ok {
+		t.Error("Expected expired token to not be returned")
+	}
+}
 
-	// Note: LoadWebhookSecret tries Secret Manager first, which will fail in test environment
-	// This is expected behavior - the function should handle the error gracefully
-	_ = LoadWebhookSecret(config)
+func TestLoadWebhookSecret_FromEnv(t *testing.T) {
+	testSecret := "test-webhook-secret"
+	_ = os.Setenv("WEBHOOK_SECRET", testSecret)
+	defer func() { _ = os.Unsetenv("WEBHOOK_SECRET") }()
+
+	config := &configs.Config{WebhookSecret: ""}
+	_ = LoadWebhookSecret(context.Background(), config)
 
-	// Verify the environment variable is set (even if Secret Manager fails)
 	envSecret := os.Getenv("WEBHOOK_SECRET")
 	if envSecret != testSecret {
 		t.Errorf("WEBHOOK_SECRET env var = %s, want %s", envSecret, testSecret)
 	}
-
-	// Note: In production, LoadWebhookSecret would populate config.WebhookSecret
-	// from Secret Manager or fall back to the environment variable
 }
 
 func TestLoadMongoURI_FromEnv(t *testing.T) {
-	// Test loading MongoDB URI from environment variable
 	testURI := "mongodb://localhost:27017/test"
-	os.Setenv("MONGO_URI", testURI)
-	defer os.Unsetenv("MONGO_URI")
+	_ = os.Setenv("MONGO_URI", testURI)
+	defer func() { _ = os.Unsetenv("MONGO_URI") }()
 
-	// Verify the environment variable is set
 	envURI := os.Getenv("MONGO_URI")
 	if envURI != testURI {
 		t.Errorf("MONGO_URI env var = %s, want %s", envURI, testURI)
 	}
-
-	// Note: LoadMongoURI function signature needs to be checked
-	// This test documents that MONGO_URI can be set via environment
 }
 
 func TestGitHubAppID_FromEnv(t *testing.T) {
-	// Test that GITHUB_APP_ID can be read from environment
 	testAppID := "123456"
-	os.Setenv("GITHUB_APP_ID", testAppID)
-	defer os.Unsetenv("GITHUB_APP_ID")
+	_ = os.Setenv("GITHUB_APP_ID", testAppID)
+	defer func() { _ = os.Unsetenv("GITHUB_APP_ID") }()
 
 	appID := os.Getenv("GITHUB_APP_ID")
 	if appID != testAppID {
@@ -119,10 +181,9 @@ func TestGitHubAppID_FromEnv(t *testing.T) {
 }
 
 func TestGitHubInstallationID_FromEnv(t *testing.T) {
-	// Test that GITHUB_INSTALLATION_ID can be read from environment
 	testInstallID := "789012"
-	os.Setenv("GITHUB_INSTALLATION_ID", testInstallID)
-	defer os.Unsetenv("GITHUB_INSTALLATION_ID")
+	_ = os.Setenv("GITHUB_INSTALLATION_ID", testInstallID)
+	defer func() { _ = os.Unsetenv("GITHUB_INSTALLATION_ID") }()
 
 	installID := os.Getenv("GITHUB_INSTALLATION_ID")
 	if installID != testInstallID {
@@ -131,10 +192,9 @@ func TestGitHubInstallationID_FromEnv(t *testing.T) {
 }
 
 func TestGitHubPrivateKeyPath_FromEnv(t *testing.T) {
-	// Test that GITHUB_PRIVATE_KEY_PATH can be read from environment
 	testPath := "/path/to/private-key.pem"
-	os.Setenv("GITHUB_PRIVATE_KEY_PATH", testPath)
-	defer os.Unsetenv("GITHUB_PRIVATE_KEY_PATH")
+	_ = os.Setenv("GITHUB_PRIVATE_KEY_PATH", testPath)
+	defer func() { _ = os.Unsetenv("GITHUB_PRIVATE_KEY_PATH") }()
 
 	keyPath := os.Getenv("GITHUB_PRIVATE_KEY_PATH")
 	if keyPath != testPath {
@@ -142,83 +202,320 @@ func TestGitHubPrivateKeyPath_FromEnv(t *testing.T) {
 	}
 }
 
-func TestInstallationAccessToken_GlobalVariable(t *testing.T) {
-	// Test that we can manipulate the global InstallationAccessToken
-	originalToken := InstallationAccessToken
-	defer func() {
-		InstallationAccessToken = originalToken
-	}()
+func TestTokenManager_InstallationAccessToken(t *testing.T) {
+	tm := NewTokenManager()
 
-	testToken := "ghs_test_token_123"
-	InstallationAccessToken = testToken
+	if got := tm.GetInstallationAccessToken(); got != "" {
+		t.Errorf("Expected empty token, got %q", got)
+	}
 
-	if InstallationAccessToken != testToken {
-		t.Errorf("InstallationAccessToken = %s, want %s", InstallationAccessToken, testToken)
+	tm.SetInstallationAccessToken("ghs_test_token_123")
+	if got := tm.GetInstallationAccessToken(); got != "ghs_test_token_123" {
+		t.Errorf("InstallationAccessToken = %s, want ghs_test_token_123", got)
 	}
 }
 
-func TestHTTPClient_GlobalVariable(t *testing.T) {
-	// Test that HTTPClient is initialized
-	if HTTPClient == nil {
+func TestTokenManager_HTTPClient(t *testing.T) {
+	tm := NewTokenManager()
+
+	// Default client should not be nil
+	if tm.GetHTTPClient() == nil {
 		t.Error("HTTPClient should not be nil")
 	}
 
-	// Note: HTTPClient is initialized to http.DefaultClient which has Timeout = 0 (no timeout)
-	// This is the default behavior in Go's http package
-	// The test just verifies the client exists
+	// Should be able to swap clients
+	custom := &http.Client{}
+	tm.SetHTTPClient(custom)
+	if tm.GetHTTPClient() != custom {
+		t.Error("Expected custom HTTP client after SetHTTPClient")
+	}
 }
 
-func TestJWTExpiry_GlobalVariable(t *testing.T) {
-	// Test that we can manipulate the JWT expiry time
-	originalExpiry := jwtExpiry
-	defer func() {
-		jwtExpiry = originalExpiry
-	}()
+func TestTokenManager_JWTExpiry(t *testing.T) {
+	tm := NewTokenManager()
 
-	// Set a future expiry
 	futureExpiry := time.Now().Add(1 * time.Hour)
-	jwtExpiry = futureExpiry
-
-	if time.Now().After(jwtExpiry) {
+	tm.SetCachedJWT("future-jwt", futureExpiry)
+	_, ok := tm.GetCachedJWT()
+	if !ok {
 		t.Error("JWT should not be expired")
 	}
 
-	// Set a past expiry
 	pastExpiry := time.Now().Add(-1 * time.Hour)
-	jwtExpiry = pastExpiry
-
-	if !time.Now().After(jwtExpiry) {
+	tm.SetCachedJWT("past-jwt", pastExpiry)
+	_, ok = tm.GetCachedJWT()
+	if ok {
 		t.Error("JWT should be expired")
 	}
 }
 
-// TODO https://jira.mongodb.org/browse/DOCSP-54727
-// Note: Comprehensive testing of github_auth.go would require:
-// 1. Mocking the Secret Manager client
-// 2. Mocking the GitHub API client
-// 3. Testing the full authentication flow:
-//    - JWT generation with valid PEM key
-//    - Installation token retrieval
-//    - Token caching and refresh logic
-//    - Organization-specific client creation
-//    - Error handling for API failures
-//
-// Example test scenarios that would require mocking:
-// - TestConfigurePermissions_Success
-// - TestConfigurePermissions_MissingAppID
-// - TestConfigurePermissions_InvalidPEM
-// - TestGetInstallationAccessToken_Success
-// - TestGetInstallationAccessToken_Cached
-// - TestGetInstallationAccessToken_Expired
-// - TestGetRestClientForOrg_Success
-// - TestGetRestClientForOrg_Cached
-// - TestGetPrivateKeyFromSecret_SecretManager
-// - TestGetPrivateKeyFromSecret_LocalFile
-// - TestGetPrivateKeyFromSecret_EnvVar
-//
-// Refactoring suggestions for better testability:
-// 1. Accept Secret Manager client as parameter instead of creating it internally
-// 2. Accept GitHub client factory as parameter
-// 3. Return errors instead of calling log.Fatal
-// 4. Use dependency injection for HTTP client
-// 5. Make JWT generation and caching logic more modular
+func TestTokenManager_ThreadSafety(t *testing.T) {
+	tm := NewTokenManager()
+
+	done := make(chan bool, 10)
+
+	for i := range 5 {
+		go func(n int) {
+			defer func() { done <- true }()
+			org := "org-" + string(rune('A'+n))
+			tm.SetTokenForOrg(org, "token-"+org, time.Now().Add(1*time.Hour))
+			tm.SetCachedJWT("jwt-"+org, time.Now().Add(9*time.Minute))
+			tm.SetInstallationAccessToken("iat-" + org)
+		}(i)
+	}
+
+	for i := range 5 {
+		go func(n int) {
+			defer func() { done <- true }()
+			org := "org-" + string(rune('A'+n))
+			_, _ = tm.GetTokenForOrg(org)
+			_, _ = tm.GetCachedJWT()
+			_ = tm.GetInstallationAccessToken()
+			_ = tm.GetHTTPClient()
+		}(i)
+	}
+
+	for i := 0; i < 10; i++ {
+		<-done
+	}
+}
+
+func TestGetInstallationAccessToken_Success(t *testing.T) {
+	c := &http.Client{}
+	httpmock.ActivateNonDefault(c)
+	t.Cleanup(httpmock.DeactivateAndReset)
+
+	httpmock.RegisterResponder("POST",
+		"https://api.github.com/app/installations/12345/access_tokens",
+		httpmock.NewJsonResponderOrPanic(201, map[string]any{
+			"token":      "ghs_test123",
+			"expires_at": "2030-01-01T00:00:00Z",
+		}),
+	)
+
+	token, expiresAt, err := getInstallationAccessToken("12345", "fake-jwt", c)
+	if err != nil {
+		t.Fatalf("getInstallationAccessToken: %v", err)
+	}
+	if token != "ghs_test123" {
+		t.Errorf("token = %q, want ghs_test123", token)
+	}
+	if expiresAt.IsZero() {
+		t.Error("expected non-zero expiresAt")
+	}
+}
+
+func TestGetInstallationAccessToken_MissingInstallationID(t *testing.T) {
+	_, _, err := getInstallationAccessToken("", "fake-jwt", nil)
+	if err == nil {
+		t.Error("expected error with empty installation ID")
+	}
+}
+
+func TestGetInstallationAccessToken_Unauthorized(t *testing.T) {
+	c := &http.Client{}
+	httpmock.ActivateNonDefault(c)
+	t.Cleanup(httpmock.DeactivateAndReset)
+
+	httpmock.RegisterResponder("POST",
+		"https://api.github.com/app/installations/12345/access_tokens",
+		httpmock.NewJsonResponderOrPanic(401, map[string]any{
+			"message": "Bad credentials",
+		}),
+	)
+
+	_, _, err := getInstallationAccessToken("12345", "bad-jwt", c)
+	if err == nil {
+		t.Fatal("expected error on 401")
+	}
+	if !errors.Is(err, ErrAuthentication) {
+		t.Errorf("expected ErrAuthentication, got: %v", err)
+	}
+}
+
+func TestConfigurePermissions_FullFlow(t *testing.T) {
+	// Generate a real RSA key for JWT signing
+	key, _ := rsa.GenerateKey(rand.Reader, 2048)
+	der := x509.MarshalPKCS1PrivateKey(key)
+	pemBytes := pem.EncodeToMemory(&pem.Block{Type: "RSA PRIVATE KEY", Bytes: der})
+
+	t.Setenv("SKIP_SECRET_MANAGER", "true")
+	t.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
+
+	// Use a fresh TokenManager to avoid polluting other tests
+	tm := NewTokenManager()
+	prev := defaultTokenManager
+	defaultTokenManager = tm
+	t.Cleanup(func() { defaultTokenManager = prev })
+
+	c := &http.Client{}
+	httpmock.ActivateNonDefault(c)
+	t.Cleanup(httpmock.DeactivateAndReset)
+	tm.SetHTTPClient(c)
+
+	httpmock.RegisterResponder("POST",
+		"https://api.github.com/app/installations/99999/access_tokens",
+		httpmock.NewJsonResponderOrPanic(201, map[string]any{
+			"token":      "ghs_configured_token",
+			"expires_at": "2030-01-01T00:00:00Z",
+		}),
+	)
+
+	config := &configs.Config{
+		AppId:          "123456",
+		InstallationId: "99999",
+	}
+
+	err := ConfigurePermissions(context.Background(), config)
+	if err != nil {
+		t.Fatalf("ConfigurePermissions: %v", err)
+	}
+
+	if got := tm.GetInstallationAccessToken(); got != "ghs_configured_token" {
+		t.Errorf("installation token = %q, want ghs_configured_token", got)
+	}
+
+	// Verify the token endpoint was called exactly once
+	info := httpmock.GetCallCountInfo()
+	if info["POST https://api.github.com/app/installations/99999/access_tokens"] != 1 {
+		t.Errorf("expected exactly 1 call to token endpoint, got %d",
+			info["POST https://api.github.com/app/installations/99999/access_tokens"])
+	}
+}
+
+func TestGetPrivateKeyFromSecret_EnvVar(t *testing.T) {
+	key, _ := rsa.GenerateKey(rand.Reader, 2048)
+	der := x509.MarshalPKCS1PrivateKey(key)
+	pemBytes := pem.EncodeToMemory(&pem.Block{Type: "RSA PRIVATE KEY", Bytes: der})
+
+	t.Setenv("SKIP_SECRET_MANAGER", "true")
+	t.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
+
+	got, err := getPrivateKeyFromSecret(context.Background(), &configs.Config{})
+	if err != nil {
+		t.Fatalf("getPrivateKeyFromSecret: %v", err)
+	}
+	if string(got) != string(pemBytes) {
+		t.Error("returned key does not match expected PEM bytes")
+	}
+}
+
+func TestGetPrivateKeyFromSecret_Base64(t *testing.T) {
+	key, _ := rsa.GenerateKey(rand.Reader, 2048)
+	der := x509.MarshalPKCS1PrivateKey(key)
+	pemBytes := pem.EncodeToMemory(&pem.Block{Type: "RSA PRIVATE KEY", Bytes: der})
+
+	t.Setenv("SKIP_SECRET_MANAGER", "true")
+	// Clear direct env var to force base64 path
+	t.Setenv("GITHUB_APP_PRIVATE_KEY", "")
+	t.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
+
+	got, err := getPrivateKeyFromSecret(context.Background(), &configs.Config{})
+	if err != nil {
+		t.Fatalf("getPrivateKeyFromSecret: %v", err)
+	}
+	if string(got) != string(pemBytes) {
+		t.Error("returned key does not match expected PEM bytes")
+	}
+}
+
+func TestGetPrivateKeyFromSecret_MissingAllEnvVars(t *testing.T) {
+	t.Setenv("SKIP_SECRET_MANAGER", "true")
+	t.Setenv("GITHUB_APP_PRIVATE_KEY", "")
+	t.Setenv("GITHUB_APP_PRIVATE_KEY_B64", "")
+
+	_, err := getPrivateKeyFromSecret(context.Background(), &configs.Config{})
+	if err == nil {
+		t.Error("expected error when no key env vars set")
+	}
+	if !errors.Is(err, ErrSecretAccess) {
+		t.Errorf("expected ErrSecretAccess, got: %v", err)
+	}
+}
+
+func TestGetInstallationIDForOrg_Success(t *testing.T) {
+	// Set up a fresh TokenManager with a cached JWT to avoid private key lookup
+	tm := NewTokenManager()
+	tm.SetCachedJWT("fake-jwt", time.Now().Add(5*time.Minute))
+	prev := defaultTokenManager
+	defaultTokenManager = tm
+	t.Cleanup(func() { defaultTokenManager = prev })
+
+	c := &http.Client{}
+	httpmock.ActivateNonDefault(c)
+	t.Cleanup(httpmock.DeactivateAndReset)
+	tm.SetHTTPClient(c)
+
+	httpmock.RegisterResponder("GET", "https://api.github.com/app/installations",
+		httpmock.NewJsonResponderOrPanic(200, []map[string]any{
+			{"id": 111, "account": map[string]any{"login": "org-a", "type": "Organization"}},
+			{"id": 222, "account": map[string]any{"login": "org-b", "type": "Organization"}},
+		}),
+	)
+
+	config := &configs.Config{AppId: "123"}
+
+	id, err := getInstallationIDForOrg(context.Background(), config, "org-b")
+	if err != nil {
+		t.Fatalf("getInstallationIDForOrg: %v", err)
+	}
+	if id != "222" {
+		t.Errorf("installationID = %q, want 222", id)
+	}
+}
+
+func TestGetInstallationIDForOrg_NotFound(t *testing.T) {
+	tm := NewTokenManager()
+	tm.SetCachedJWT("fake-jwt", time.Now().Add(5*time.Minute))
+	prev := defaultTokenManager
+	defaultTokenManager = tm
+	t.Cleanup(func() { defaultTokenManager = prev })
+
+	c := &http.Client{}
+	httpmock.ActivateNonDefault(c)
+	t.Cleanup(httpmock.DeactivateAndReset)
+	tm.SetHTTPClient(c)
+
+	httpmock.RegisterResponder("GET", "https://api.github.com/app/installations",
+		httpmock.NewJsonResponderOrPanic(200, []map[string]any{
+			{"id": 111, "account": map[string]any{"login": "org-a", "type": "Organization"}},
+		}),
+	)
+
+	config := &configs.Config{AppId: "123"}
+
+	_, err := getInstallationIDForOrg(context.Background(), config, "no-such-org")
+	if err == nil {
+		t.Fatal("expected error for unknown org")
+	}
+	if !errors.Is(err, ErrInstallationNotFound) {
+		t.Errorf("expected ErrInstallationNotFound, got: %v", err)
+	}
+}
+
+func TestGetInstallationIDForOrg_Unauthorized(t *testing.T) {
+	tm := NewTokenManager()
+	tm.SetCachedJWT("bad-jwt", time.Now().Add(5*time.Minute))
+	prev := defaultTokenManager
+	defaultTokenManager = tm
+	t.Cleanup(func() { defaultTokenManager = prev })
+
+	c := &http.Client{}
+	httpmock.ActivateNonDefault(c)
+	t.Cleanup(httpmock.DeactivateAndReset)
+	tm.SetHTTPClient(c)
+
+	httpmock.RegisterResponder("GET", "https://api.github.com/app/installations",
+		httpmock.NewJsonResponderOrPanic(401, map[string]any{"message": "Bad credentials"}),
+	)
+
+	config := &configs.Config{AppId: "123"}
+
+	_, err := getInstallationIDForOrg(context.Background(), config, "org-a")
+	if err == nil {
+		t.Fatal("expected error on 401")
+	}
+	if !errors.Is(err, ErrAuthentication) {
+		t.Errorf("expected ErrAuthentication, got: %v", err)
+	}
+}
diff --git a/services/github_read.go b/services/github_read.go
index e213712..4fa4d5a 100644
--- a/services/github_read.go
+++ b/services/github_read.go
@@ -3,12 +3,10 @@ package services
 import (
 	"context"
 	"fmt"
-	"log"
-	"os"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/configs"
-	. "github.com/grove-platform/github-copier/types"
+	"github.com/grove-platform/github-copier/types"
 	"github.com/shurcooL/githubv4"
 )
 
@@ -18,27 +16,27 @@ import (
 //   - owner: The repository owner (e.g., "mongodb")
 //   - repo: The repository name (e.g., "docs-sample-apps")
 //   - pr_number: The pull request number
-func GetFilesChangedInPr(owner string, repo string, pr_number int) ([]ChangedFile, error) {
-	if InstallationAccessToken == "" {
-		log.Println("No installation token provided")
-		if err := ConfigurePermissions(); err != nil {
+func GetFilesChangedInPr(ctx context.Context, config *configs.Config, owner string, repo string, pr_number int) ([]types.ChangedFile, error) {
+	if defaultTokenManager.GetInstallationAccessToken() == "" {
+		LogWarning("No installation token provided, configuring permissions")
+		if err := ConfigurePermissions(ctx, config); err != nil {
 			return nil, fmt.Errorf("failed to configure permissions: %w", err)
 		}
 	}
 
-	client, err := GetGraphQLClient()
+	// Use org-specific client to ensure we have the right installation token
+	client, err := GetGraphQLClientForOrg(ctx, config, owner)
 	if err != nil {
-		return nil, fmt.Errorf("failed to get GraphQL client: %w", err)
+		return nil, fmt.Errorf("failed to get GraphQL client for org %s: %w", owner, err)
 	}
-	ctx := context.Background()
 
-	var changedFiles []ChangedFile
+	var changedFiles []types.ChangedFile
 	var cursor *githubv4.String = nil
 	hasNextPage := true
 
 	// Paginate through all files
 	for hasNextPage {
-		var prQuery PullRequestQuery
+		var prQuery types.PullRequestQuery
 		variables := map[string]interface{}{
 			"owner":  githubv4.String(owner),
 			"name":   githubv4.String(repo),
@@ -48,16 +46,16 @@ func GetFilesChangedInPr(owner string, repo string, pr_number int) ([]ChangedFil
 
 		err := client.Query(ctx, &prQuery, variables)
 		if err != nil {
-			LogCritical(fmt.Sprintf("Failed to execute query GetFilesChanged: %v", err))
+			LogCritical("Failed to execute query GetFilesChanged", "error", err)
 			return nil, err
 		}
 
 		// Append files from this page
 		for _, edge := range prQuery.Repository.PullRequest.Files.Edges {
-			changedFiles = append(changedFiles, ChangedFile{
+			changedFiles = append(changedFiles, types.ChangedFile{
 				Path:      string(edge.Node.Path),
-				Additions: int(edge.Node.Additions),
-				Deletions: int(edge.Node.Deletions),
+				Additions: int(edge.Node.Additions), // #nosec G115 -- PR additions/deletions fit in int
+				Deletions: int(edge.Node.Deletions), // #nosec G115 -- PR additions/deletions fit in int
 				Status:    string(edge.Node.ChangeType),
 			})
 		}
@@ -69,52 +67,31 @@ func GetFilesChangedInPr(owner string, repo string, pr_number int) ([]ChangedFil
 		}
 	}
 
-	LogInfo(fmt.Sprintf("PR has %d changed files.", len(changedFiles)))
-
-	// Log all files for debugging (especially to see if server files are included)
-	LogInfo("=== ALL FILES FROM GRAPHQL API ===")
-	for i, file := range changedFiles {
-		LogInfo(fmt.Sprintf("  [%d] %s (status: %s)", i, file.Path, file.Status))
-	}
-	LogInfo("=== END FILE LIST ===")
-
-	// Count files by directory for debugging
-	clientCount := 0
-	serverCount := 0
-	otherCount := 0
-	for _, file := range changedFiles {
-		if len(file.Path) >= 13 && file.Path[:13] == "mflix/client/" {
-			clientCount++
-		} else if len(file.Path) >= 13 && file.Path[:13] == "mflix/server/" {
-			serverCount++
-		} else {
-			otherCount++
-		}
-	}
-	LogInfo(fmt.Sprintf("File breakdown: client=%d, server=%d, other=%d", clientCount, serverCount, otherCount))
+	LogInfoCtx(ctx, "Retrieved changed files from PR", map[string]interface{}{
+		"file_count": len(changedFiles),
+	})
 
 	return changedFiles, nil
 }
 
 // RetrieveFileContents fetches the contents of a file from the config repository at the specified path.
 // It returns a github.RepositoryContent object containing the file details.
-func RetrieveFileContents(filePath string) (github.RepositoryContent, error) {
-	owner := os.Getenv(configs.ConfigRepoOwner)
-	repo := os.Getenv(configs.ConfigRepoName)
+func RetrieveFileContents(ctx context.Context, config *configs.Config, filePath string) (github.RepositoryContent, error) {
+	owner := config.ConfigRepoOwner
+	repo := config.ConfigRepoName
 	client := GetRestClient()
-	ctx := context.Background()
 
 	fileContent, _, _, err :=
 		client.Repositories.GetContents(ctx, owner, repo,
 			filePath, &github.RepositoryContentGetOptions{
-				Ref: os.Getenv(configs.ConfigRepoBranch),
+				Ref: config.ConfigRepoBranch,
 			})
 
 	if err != nil {
 		return github.RepositoryContent{}, fmt.Errorf("failed to get file content for %s: %w", filePath, err)
 	}
 	if fileContent == nil {
-		return github.RepositoryContent{}, fmt.Errorf("file content is nil for path: %s", filePath)
+		return github.RepositoryContent{}, fmt.Errorf("%w: %s", ErrContentNil, filePath)
 	}
 	return *fileContent, nil
 }
diff --git a/services/github_read_test.go b/services/github_read_test.go
index 3f79a59..6a3fd18 100644
--- a/services/github_read_test.go
+++ b/services/github_read_test.go
@@ -1,10 +1,11 @@
 package services_test
 
 import (
+	"context"
 	"encoding/base64"
 	"testing"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/services"
 	"github.com/stretchr/testify/require"
 
@@ -99,7 +100,8 @@ func TestRetrieveFileContents_Success(t *testing.T) {
 	payload := "hello"
 	stubContentsForBothOwners(path, b64(payload), owner, repo)
 
-	rc, err := services.RetrieveFileContents(path)
+	cfg := test.TestConfig()
+	rc, err := services.RetrieveFileContents(context.Background(), cfg, path)
 	require.NoError(t, err, "expected RetrieveFileContents to succeed")
 	require.IsType(t, github.RepositoryContent{}, rc)
 	require.Equal(t, path, rc.GetPath())
diff --git a/services/github_write_to_source.go b/services/github_write_to_source.go
index c1941cd..56b7300 100644
--- a/services/github_write_to_source.go
+++ b/services/github_write_to_source.go
@@ -4,36 +4,46 @@ import (
 	"context"
 	"encoding/json"
 	"fmt"
-	"os"
 	"time"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/configs"
-	. "github.com/grove-platform/github-copier/types"
+	"github.com/grove-platform/github-copier/types"
 )
 
-func UpdateDeprecationFile() {
+// UpdateDeprecationFile updates the deprecation file with the provided data map.
+func UpdateDeprecationFile(ctx context.Context, config *configs.Config, filesToDeprecate map[string]types.Configs) {
 	// Early return if there are no files to deprecate - prevents blank commits
-	if len(FilesToDeprecate) == 0 {
+	if len(filesToDeprecate) == 0 {
 		LogInfo("No deprecated files to record; skipping deprecation file update")
 		return
 	}
 
+	if config.DryRun {
+		LogInfo("[DRY-RUN] Would update deprecation file",
+			"file", config.DeprecationFile,
+			"deprecated_count", len(filesToDeprecate),
+		)
+		for path := range filesToDeprecate {
+			LogInfo("[DRY-RUN] Would mark as deprecated", "path", path)
+		}
+		return
+	}
+
 	// Fetch the deprecation file from the repository
 	client := GetRestClient()
-	ctx := context.Background()
 
 	fileContent, _, _, err := client.Repositories.GetContents(
 		ctx,
-		os.Getenv(configs.ConfigRepoOwner),
-		os.Getenv(configs.ConfigRepoName),
-		os.Getenv(configs.DeprecationFile),
+		config.ConfigRepoOwner,
+		config.ConfigRepoName,
+		config.DeprecationFile,
 		&github.RepositoryContentGetOptions{
-			Ref: os.Getenv(configs.ConfigRepoBranch),
+			Ref: config.ConfigRepoBranch,
 		},
 	)
 	if err != nil {
-		LogError(fmt.Sprintf("Error getting deprecation file: %v", err))
+		LogError("Error getting deprecation file", "error", err)
 		return
 	}
 	if fileContent == nil {
@@ -43,19 +53,19 @@ func UpdateDeprecationFile() {
 
 	content, err := fileContent.GetContent()
 	if err != nil {
-		LogError(fmt.Sprintf("Error decoding deprecation file: %v", err))
+		LogError("Error decoding deprecation file", "error", err)
 		return
 	}
 
-	var deprecationFile DeprecationFile
+	var deprecationFile types.DeprecationFile
 	err = json.Unmarshal([]byte(content), &deprecationFile)
 	if err != nil {
-		LogError(fmt.Sprintf("Failed to unmarshal %s: %v", configs.DeprecationFile, err))
+		LogError("Failed to unmarshal deprecation file", "file", config.DeprecationFile, "error", err)
 		return
 	}
 
-	for key, value := range FilesToDeprecate {
-		newDeprecatedFileEntry := DeprecatedFileEntry{
+	for key, value := range filesToDeprecate {
+		newDeprecatedFileEntry := types.DeprecatedFileEntry{
 			FileName:  key,
 			Repo:      value.TargetRepo,
 			Branch:    value.TargetBranch,
@@ -66,24 +76,24 @@ func UpdateDeprecationFile() {
 
 	updatedJSON, err := json.MarshalIndent(deprecationFile, "", "  ")
 	if err != nil {
-		LogError(fmt.Sprintf("Error marshaling JSON: %v", err))
+		LogError("Error marshaling JSON", "error", err)
+		return
 	}
 
-	message := fmt.Sprintf("Updating %s.", os.Getenv(configs.DeprecationFile))
-	uploadDeprecationFileChanges(message, string(updatedJSON))
+	message := fmt.Sprintf("Updating %s.", config.DeprecationFile)
+	uploadDeprecationFileChanges(ctx, config, message, string(updatedJSON))
 
-	LogInfo(fmt.Sprintf("Successfully updated %s with %d entries", os.Getenv(configs.DeprecationFile), len(FilesToDeprecate)))
+	LogInfo("Successfully updated deprecation file", "file", config.DeprecationFile, "entries", len(filesToDeprecate))
 }
 
-func uploadDeprecationFileChanges(message string, newDeprecationFileContents string) {
+func uploadDeprecationFileChanges(ctx context.Context, config *configs.Config, message string, newDeprecationFileContents string) {
 	client := GetRestClient()
-	ctx := context.Background()
 
-	targetFileContent, _, _, err := client.Repositories.GetContents(ctx, os.Getenv(configs.ConfigRepoOwner), os.Getenv(configs.ConfigRepoName),
-		os.Getenv(configs.DeprecationFile), &github.RepositoryContentGetOptions{Ref: os.Getenv(configs.ConfigRepoBranch)})
+	targetFileContent, _, _, err := client.Repositories.GetContents(ctx, config.ConfigRepoOwner, config.ConfigRepoName,
+		config.DeprecationFile, &github.RepositoryContentGetOptions{Ref: config.ConfigRepoBranch})
 
 	if err != nil {
-		LogError(fmt.Sprintf("Error getting deprecation file contents: %v", err))
+		LogError("Error getting deprecation file contents", "error", err)
 		return
 	}
 	if targetFileContent == nil {
@@ -92,17 +102,17 @@ func uploadDeprecationFileChanges(message string, newDeprecationFileContents str
 	}
 
 	options := &github.RepositoryContentFileOptions{
-		Message: github.String(message),
+		Message: github.Ptr(message),
 		Content: []byte(newDeprecationFileContents),
-		Branch:  github.String(os.Getenv(configs.ConfigRepoBranch)),
-		Committer: &github.CommitAuthor{Name: github.String(os.Getenv(configs.CommitterName)),
-			Email: github.String(os.Getenv(configs.CommitterEmail))},
+		Branch:  github.Ptr(config.ConfigRepoBranch),
+		Committer: &github.CommitAuthor{Name: github.Ptr(config.CommitterName),
+			Email: github.Ptr(config.CommitterEmail)},
 	}
 
 	options.SHA = targetFileContent.SHA
-	_, _, err = client.Repositories.UpdateFile(ctx, os.Getenv(configs.ConfigRepoOwner), os.Getenv(configs.ConfigRepoName), os.Getenv(configs.DeprecationFile), options)
+	_, _, err = client.Repositories.UpdateFile(ctx, config.ConfigRepoOwner, config.ConfigRepoName, config.DeprecationFile, options)
 	if err != nil {
-		LogError(fmt.Sprintf("Cannot update deprecation file: %v", err))
+		LogError("Cannot update deprecation file", "error", err)
 	}
 
 	LogInfo("Deprecation file updated.")
diff --git a/services/github_write_to_source_test.go b/services/github_write_to_source_test.go
index c9af808..7a92bf2 100644
--- a/services/github_write_to_source_test.go
+++ b/services/github_write_to_source_test.go
@@ -1,92 +1,28 @@
 package services
 
 import (
+	"context"
 	"testing"
 
-	. "github.com/grove-platform/github-copier/types"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/types"
 )
 
-func TestUpdateDeprecationFile_EmptyList(t *testing.T) {
-	// When FilesToDeprecate is empty, UpdateDeprecationFile should return early
-	// FilesToDeprecate is a map[string]Configs
-	originalFiles := FilesToDeprecate
-	defer func() {
-		FilesToDeprecate = originalFiles
-	}()
-
-	FilesToDeprecate = make(map[string]Configs)
-
-	// This should not panic or error - it should return early
-	// Note: This test doesn't verify the actual GitHub API call since that would
-	// require mocking the GitHub client, which is a global variable
-	UpdateDeprecationFile()
-
-	// If we get here without panic, the test passes
+func TestUpdateDeprecationFile_EmptyMap(t *testing.T) {
+	// When the map is empty, UpdateDeprecationFile should return early without panic.
+	UpdateDeprecationFile(context.Background(), configs.NewConfig(), map[string]types.Configs{})
 }
 
 func TestUpdateDeprecationFile_WithFiles(t *testing.T) {
-	// Set up files to deprecate
-	originalFiles := FilesToDeprecate
-	defer func() {
-		FilesToDeprecate = originalFiles
-	}()
-
-	FilesToDeprecate = map[string]Configs{
-		"examples/old-example.go": {
-			TargetRepo:   "test/target",
-			TargetBranch: "main",
-		},
-		"examples/deprecated.go": {
-			TargetRepo:   "test/target",
-			TargetBranch: "main",
-		},
-	}
-
-	// Note: This test will fail if it actually tries to call GitHub API
+	// Note: This test will fail if it actually tries to call GitHub API.
 	// In a real test environment, we would need to:
 	// 1. Mock the GetRestClient() function
 	// 2. Mock the GitHub API responses
 	// 3. Verify the correct API calls were made
-	//
-	// For now, this test documents the expected behavior
-	// The actual implementation would require refactoring to inject dependencies
-
-	// Since we can't easily test this without mocking, we'll skip the actual call
 	t.Skip("Skipping test that requires GitHub API mocking")
 }
 
-func TestFilesToDeprecate_GlobalVariable(t *testing.T) {
-	// Test that we can manipulate the global FilesToDeprecate variable
-	originalFiles := FilesToDeprecate
-	defer func() {
-		FilesToDeprecate = originalFiles
-	}()
-
-	// Set test files (FilesToDeprecate is a map[string]Configs)
-	testFiles := map[string]Configs{
-		"file1.go": {TargetRepo: "test/repo1", TargetBranch: "main"},
-		"file2.go": {TargetRepo: "test/repo2", TargetBranch: "develop"},
-		"file3.go": {TargetRepo: "test/repo3", TargetBranch: "main"},
-	}
-	FilesToDeprecate = testFiles
-
-	if len(FilesToDeprecate) != 3 {
-		t.Errorf("FilesToDeprecate length = %d, want 3", len(FilesToDeprecate))
-	}
-
-	for file, config := range testFiles {
-		if deprecatedConfig, exists := FilesToDeprecate[file]; !exists {
-			t.Errorf("FilesToDeprecate missing file %s", file)
-		} else if deprecatedConfig.TargetRepo != config.TargetRepo {
-			t.Errorf("FilesToDeprecate[%s].TargetRepo = %s, want %s", file, deprecatedConfig.TargetRepo, config.TargetRepo)
-		}
-	}
-}
-
 func TestDeprecationFileEnvironmentVariables(t *testing.T) {
-	// Test that deprecation file configuration can be set via environment variables
-	// The UpdateDeprecationFile function uses os.Getenv to read these values
-
 	tests := []struct {
 		name            string
 		deprecationFile string
@@ -107,8 +43,6 @@ func TestDeprecationFileEnvironmentVariables(t *testing.T) {
 
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			// The deprecation file path is typically configured via environment variables
-			// This test documents the expected configuration approach
 			if tt.deprecationFile == "" {
 				t.Error("Deprecation file path should not be empty")
 			}
diff --git a/services/github_write_to_target.go b/services/github_write_to_target.go
index e77066e..11c6e88 100644
--- a/services/github_write_to_target.go
+++ b/services/github_write_to_target.go
@@ -4,152 +4,168 @@ import (
 	"context"
 	"fmt"
 	"net/http"
-	"os"
 	"strings"
 	"time"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/configs"
-	. "github.com/grove-platform/github-copier/types"
-	"github.com/pkg/errors"
+	"github.com/grove-platform/github-copier/types"
 )
 
-// FilesToUpload is a map where the key is the repo name
-// and the value is of type [UploadFileContent], which
-// contains the target branch name and the collection of files
-// to be uploaded.
-var FilesToUpload map[UploadKey]UploadFileContent
-var FilesToDeprecate map[string]Configs
-
-// repoOwner returns the config repository owner from environment variables.
-func repoOwner() string { return os.Getenv(configs.ConfigRepoOwner) }
-
 // parseRepoPath parses a repository path in the format "owner/repo" and returns owner and repo separately.
-// If the path doesn't contain a slash, it returns the source repo owner from env and the path as repo name.
-func parseRepoPath(repoPath string) (owner, repo string) {
+// If the path doesn't contain a slash, it returns defaultOwner and the path as repo name.
+func parseRepoPath(repoPath string, defaultOwner string) (owner, repo string) {
 	parts := strings.Split(repoPath, "/")
 	if len(parts) == 2 {
 		return parts[0], parts[1]
 	}
-	// Fallback to source repo owner if no slash found (backward compatibility)
-	return repoOwner(), repoPath
+	// Fallback to default owner if no slash found (backward compatibility)
+	return defaultOwner, repoPath
 }
 
 // normalizeRepoName ensures a repository name includes the owner prefix.
 // If the repo name already has an owner (contains "/"), returns it as-is.
-// Otherwise, prepends the default repo owner from environment.
-func normalizeRepoName(repoName string) string {
+// Otherwise, prepends the defaultOwner.
+func normalizeRepoName(repoName string, defaultOwner string) string {
 	if strings.Contains(repoName, "/") {
 		return repoName
 	}
-	return repoOwner() + "/" + repoName
+	return defaultOwner + "/" + repoName
 }
 
-// AddFilesToTargetRepoBranch uploads files to the target repository branch
-// using the specified commit strategy (direct or via pull request).
-func AddFilesToTargetRepoBranch() {
-	AddFilesToTargetRepoBranchWithFetcher(nil, nil)
-}
+// normalizeRefPath ensures a ref path is in the correct format for different GitHub API calls.
+// For GetRef: expects "heads/main" (no "refs/" prefix)
+// For UpdateRef: expects "refs/heads/main" (full ref path)
+func normalizeRefPath(branchPath string, fullPath bool) string {
+	// Strip "refs/" prefix if present
+	refPath := strings.TrimPrefix(branchPath, "refs/")
 
-// AddFilesToTargetRepoBranchWithFetcher uploads files to the target repository branch
-// using the specified commit strategy (direct or via pull request).
-// If prTemplateFetcher is provided, it will be used to fetch PR templates when use_pr_template is true.
-// If metricsCollector is provided, it will be used to record upload failures.
-func AddFilesToTargetRepoBranchWithFetcher(prTemplateFetcher PRTemplateFetcher, metricsCollector *MetricsCollector) {
-	ctx := context.Background()
+	// Ensure "heads/" prefix exists (unless it's a tag)
+	if !strings.HasPrefix(refPath, "heads/") && !strings.HasPrefix(refPath, "tags/") {
+		refPath = "heads/" + refPath
+	}
 
-	for key, value := range FilesToUpload {
-		// Parse the repository to get the organization
-		owner, _ := parseRepoPath(key.RepoName)
+	// Add "refs/" prefix back if full path is needed
+	if fullPath {
+		return "refs/" + refPath
+	}
+	return refPath
+}
 
-		// Get a client authenticated for this organization
-		client, err := GetRestClientForOrg(owner)
-		if err != nil {
-			LogCritical(fmt.Sprintf("Failed to get GitHub client for org %s: %v", owner, err))
-			// Record failure for each file in this batch
-			if metricsCollector != nil {
-				for range value.Content {
-					metricsCollector.RecordFileUploadFailed()
-				}
+// AddFilesToTargetRepos uploads files to target repository branches.
+// It accepts the upload map as a parameter for concurrency safety.
+func AddFilesToTargetRepos(ctx context.Context, config *configs.Config, filesToUpload map[types.UploadKey]types.UploadFileContent, prTemplateFetcher PRTemplateFetcher, metricsCollector *MetricsCollector) {
+	if config.DryRun {
+		for key, value := range filesToUpload {
+			LogInfo("[DRY-RUN] Would upload files to target repo",
+				"repo", key.RepoName,
+				"branch", key.BranchPath,
+				"file_count", len(value.Content),
+				"strategy", value.CommitStrategy,
+			)
+			for path := range value.Content {
+				LogInfo("[DRY-RUN] Would write file", "repo", key.RepoName, "path", path)
 			}
-			continue
 		}
+		return
+	}
 
-		// Determine commit strategy from value (set by pattern-matching system)
-		strategy := string(value.CommitStrategy)
-		if strategy == "" {
-			strategy = "direct" // default
+	for key, value := range filesToUpload {
+		if err := uploadToTarget(ctx, config, key, value, prTemplateFetcher); err != nil {
+			LogCritical("Failed to upload files", "repo", key.RepoName, "error", err)
+			recordBatchFailure(metricsCollector, len(value.Content))
 		}
+	}
+}
 
-		// Get commit message from value or use default
-		commitMsg := value.CommitMessage
-		if strings.TrimSpace(commitMsg) == "" {
-			commitMsg = os.Getenv(configs.DefaultCommitMessage)
-			if strings.TrimSpace(commitMsg) == "" {
-				commitMsg = configs.NewConfig().DefaultCommitMessage
-			}
-		}
+// uploadToTarget handles a single upload-key: authenticates for the target org,
+// resolves commit parameters, and dispatches to the appropriate strategy.
+func uploadToTarget(ctx context.Context, config *configs.Config, key types.UploadKey, value types.UploadFileContent, prTemplateFetcher PRTemplateFetcher) error {
+	owner, _ := parseRepoPath(key.RepoName, config.ConfigRepoOwner)
 
-		// Get PR title from value or use commit message
-		prTitle := value.PRTitle
-		if strings.TrimSpace(prTitle) == "" {
-			prTitle = commitMsg
-		}
+	client, err := GetRestClientForOrg(ctx, config, owner)
+	if err != nil {
+		return fmt.Errorf("get GitHub client for org %s: %w", owner, err)
+	}
 
-		// Get PR body from value
-		prBody := value.PRBody
-
-		// Fetch and merge PR template if requested
-		if value.UsePRTemplate && prTemplateFetcher != nil && strategy != "direct" {
-			targetBranch := strings.TrimPrefix(key.BranchPath, "refs/heads/")
-			template, err := prTemplateFetcher.FetchPRTemplate(ctx, client, key.RepoName, targetBranch)
-			if err != nil {
-				LogWarning(fmt.Sprintf("Failed to fetch PR template for %s: %v", key.RepoName, err))
-			} else if template != "" {
-				// Merge configured body with template
-				prBody = MergePRBodyWithTemplate(prBody, template)
-				LogInfo(fmt.Sprintf("Merged PR template for %s", key.RepoName))
-			}
-		}
+	params := resolveCommitParams(config, key, value, prTemplateFetcher, client, ctx)
 
-		// Get auto-merge setting from value
-		mergeWithoutReview := value.AutoMergePR
-
-		switch strategy {
-		case "direct": // commits directly to the target branch
-			LogInfo(fmt.Sprintf("Using direct commit strategy for %s on branch %s", key.RepoName, key.BranchPath))
-			if err := addFilesToBranch(ctx, client, key, value.Content, commitMsg); err != nil {
-				LogCritical(fmt.Sprintf("Failed to add files to target branch: %v\n", err))
-				// Record failure for each file in this batch
-				if metricsCollector != nil {
-					for range value.Content {
-						metricsCollector.RecordFileUploadFailed()
-					}
-				}
-			}
-		default: // "pr" or "pull_request" strategy
-			LogInfo(fmt.Sprintf("Using PR commit strategy for %s on branch %s (auto_merge=%v)", key.RepoName, key.BranchPath, mergeWithoutReview))
-			if err := addFilesViaPR(ctx, client, key, value.Content, commitMsg, prTitle, prBody, mergeWithoutReview); err != nil {
-				LogCritical(fmt.Sprintf("Failed via PR path: %v\n", err))
-				// Record failure for each file in this batch
-				if metricsCollector != nil {
-					for range value.Content {
-						metricsCollector.RecordFileUploadFailed()
-					}
-				}
-			}
+	switch params.strategy {
+	case "direct":
+		LogInfo("Using direct commit strategy", "repo", key.RepoName, "branch", key.BranchPath)
+		return addFilesToBranch(ctx, config, client, key, value.Content, params.commitMsg)
+	default: // "pr" or "pull_request"
+		LogInfo("Using PR commit strategy", "repo", key.RepoName, "branch", key.BranchPath, "auto_merge", params.mergeWithoutReview)
+		return addFilesViaPR(ctx, config, client, key, value.Content, params.commitMsg, params.prTitle, params.prBody, params.mergeWithoutReview)
+	}
+}
+
+// commitParams groups the resolved parameters for a single upload operation.
+type commitParams struct {
+	strategy           string
+	commitMsg          string
+	prTitle            string
+	prBody             string
+	mergeWithoutReview bool
+}
+
+// resolveCommitParams derives commit strategy, message, PR title/body, and template
+// from the upload value and config defaults.
+func resolveCommitParams(config *configs.Config, key types.UploadKey, value types.UploadFileContent, prTemplateFetcher PRTemplateFetcher, client *github.Client, ctx context.Context) commitParams {
+	strategy := string(value.CommitStrategy)
+	if strategy == "" {
+		strategy = "direct"
+	}
+
+	commitMsg := value.CommitMessage
+	if strings.TrimSpace(commitMsg) == "" {
+		commitMsg = config.DefaultCommitMessage
+	}
+
+	prTitle := value.PRTitle
+	if strings.TrimSpace(prTitle) == "" {
+		prTitle = commitMsg
+	}
+
+	prBody := value.PRBody
+	if value.UsePRTemplate && prTemplateFetcher != nil && strategy != "direct" {
+		targetBranch := strings.TrimPrefix(key.BranchPath, "refs/heads/")
+		template, err := prTemplateFetcher.FetchPRTemplate(ctx, client, key.RepoName, targetBranch)
+		if err != nil {
+			LogWarning("Failed to fetch PR template", "repo", key.RepoName, "error", err)
+		} else if template != "" {
+			prBody = MergePRBodyWithTemplate(prBody, template)
+			LogInfo("Merged PR template", "repo", key.RepoName)
 		}
 	}
+
+	return commitParams{
+		strategy:           strategy,
+		commitMsg:          commitMsg,
+		prTitle:            prTitle,
+		prBody:             prBody,
+		mergeWithoutReview: value.AutoMergePR,
+	}
+}
+
+// recordBatchFailure records n file upload failures on the metrics collector.
+func recordBatchFailure(mc *MetricsCollector, n int) {
+	if mc == nil {
+		return
+	}
+	for i := 0; i < n; i++ {
+		mc.RecordFileUploadFailed()
+	}
 }
 
 // createPullRequest opens a pull request from head to base in the specified repository.
-func createPullRequest(ctx context.Context, client *github.Client, repo, head, base, title, body string) (*github.PullRequest, error) {
-	owner, repoName := parseRepoPath(repo)
+func createPullRequest(ctx context.Context, client *github.Client, defaultOwner, repo, head, base, title, body string) (*github.PullRequest, error) {
+	owner, repoName := parseRepoPath(repo, defaultOwner)
 	pr := &github.NewPullRequest{
-		Title: github.String(title),
-		Head:  github.String(head), // for same-repo branches, just "branch"; for forks, use "owner:branch"
-		Base:  github.String(base), // e.g. "main"
-		Body:  github.String(body),
+		Title: github.Ptr(title),
+		Head:  github.Ptr(head), // for same-repo branches, just "branch"; for forks, use "owner:branch"
+		Base:  github.Ptr(base), // e.g. "main"
+		Body:  github.Ptr(body),
 	}
 	created, _, err := client.PullRequests.Create(ctx, owner, repoName, pr)
 	if err != nil {
@@ -160,121 +176,130 @@ func createPullRequest(ctx context.Context, client *github.Client, repo, head, b
 
 // addFilesViaPR creates a temporary branch, commits files to it using the provided commitMessage,
 // opens a pull request with prTitle and prBody, and optionally merges it automatically.
-func addFilesViaPR(ctx context.Context, client *github.Client, key UploadKey,
+func addFilesViaPR(ctx context.Context, config *configs.Config, client *github.Client, key types.UploadKey,
 	files []github.RepositoryContent, commitMessage string, prTitle string, prBody string, mergeWithoutReview bool,
 ) error {
+	defaultOwner := config.ConfigRepoOwner
 	tempBranch := "copier/" + time.Now().UTC().Format("20060102-150405")
-
-	// 1) Create branch off the target branch specified in key.BranchPath or default to "main"
 	baseBranch := strings.TrimPrefix(key.BranchPath, "refs/heads/")
-	newRef, err := createBranch(ctx, client, key.RepoName, tempBranch, baseBranch)
-	if err != nil {
+
+	// 1. Create branch off the target
+	if _, err := createBranch(ctx, client, defaultOwner, key.RepoName, tempBranch, baseBranch); err != nil {
 		return fmt.Errorf("create branch: %w", err)
 	}
-	_ = newRef // we just need it created; ref is not reused directly
 
-	// 2) Commit files to temp branch
+	// 2. Commit files to temp branch
+	if err := commitFilesToBranch(ctx, config, client, key, files, tempBranch, commitMessage); err != nil {
+		return err
+	}
+
+	// 3. Open PR from temp branch → base branch
+	pr, err := createPullRequest(ctx, client, defaultOwner, key.RepoName, tempBranch, baseBranch, prTitle, prBody)
+	if err != nil {
+		return fmt.Errorf("create PR: %w", err)
+	}
+
+	LogInfo("PR created", "pr_number", pr.GetNumber(), "from_branch", tempBranch, "base_branch", baseBranch)
+	LogInfo("PR URL", "url", pr.GetHTMLURL())
+
+	// 4. Optionally auto-merge and clean up
+	if mergeWithoutReview {
+		return autoMergePR(ctx, config, client, key.RepoName, defaultOwner, pr.GetNumber(), tempBranch)
+	}
+	LogInfo("PR created and awaiting review", "pr_number", pr.GetNumber())
+	return nil
+}
+
+// commitFilesToBranch decodes file contents and creates a tree + commit on the temp branch.
+func commitFilesToBranch(ctx context.Context, config *configs.Config, client *github.Client, key types.UploadKey,
+	files []github.RepositoryContent, tempBranch string, commitMessage string,
+) error {
 	entries := make(map[string]string, len(files))
 	for _, f := range files {
-		content, _ := f.GetContent()
+		content, err := f.GetContent()
+		if err != nil {
+			return fmt.Errorf("decode content for %s: %w", f.GetName(), err)
+		}
 		entries[f.GetName()] = content
 	}
 
-	tempKey := UploadKey{RepoName: key.RepoName, BranchPath: "refs/heads/" + tempBranch}
-	treeSHA, baseSHA, err := createCommitTree(ctx, client, tempKey, entries)
+	tempKey := types.UploadKey{RepoName: key.RepoName, BranchPath: "refs/heads/" + tempBranch}
+	treeSHA, baseSHA, err := createCommitTree(ctx, config, client, tempKey, entries)
 	if err != nil {
 		return fmt.Errorf("create tree on temp branch: %w", err)
 	}
-	if err = createCommit(ctx, client, tempKey, baseSHA, treeSHA, commitMessage); err != nil {
+	if err = createCommit(ctx, client, config.ConfigRepoOwner, tempKey, baseSHA, treeSHA, commitMessage); err != nil {
 		return fmt.Errorf("create commit on temp branch: %w", err)
 	}
+	return nil
+}
 
-	// 3) Create PR from temp branch to base branch
-	base := strings.TrimPrefix(key.BranchPath, "refs/heads/")
-	pr, err := createPullRequest(ctx, client, key.RepoName, tempBranch, base, prTitle, prBody)
-	if err != nil {
-		return fmt.Errorf("create PR: %w", err)
+// autoMergePR polls the PR for mergeability, merges it, and deletes the temp branch.
+func autoMergePR(ctx context.Context, config *configs.Config, client *github.Client, repo string, defaultOwner string, prNumber int, tempBranch string) error {
+	owner, repoName := parseRepoPath(repo, defaultOwner)
+
+	mergeable, state := pollMergeability(ctx, client, owner, repoName, prNumber, config.PRMergePollMaxAttempts, config.PRMergePollInterval)
+	if mergeable != nil && !*mergeable || strings.EqualFold(state, "dirty") {
+		LogWarning("PR is not mergeable; leaving open for manual resolution", "pr_number", prNumber, "state", state)
+		return fmt.Errorf("%w: pull request #%d has conflicts (state=%s)", ErrMergeConflict, prNumber, state)
 	}
 
-	// 4) Optionally merge the PR without review if MergeWithoutReview is true
-	LogInfo(fmt.Sprintf("PR created: #%d from %s to %s", pr.GetNumber(), tempBranch, base))
-	LogInfo(fmt.Sprintf("PR URL: %s", pr.GetHTMLURL()))
-	if mergeWithoutReview {
-		// Poll PR for mergeability; GitHub may take a moment to compute it
-		// Get polling configuration from environment or use defaults
-		cfg := configs.NewConfig()
-		maxAttempts := cfg.PRMergePollMaxAttempts
-		if envAttempts := os.Getenv(configs.PRMergePollMaxAttempts); envAttempts != "" {
-			if parsed, err := parseIntWithDefault(envAttempts, maxAttempts); err == nil {
-				maxAttempts = parsed
-			}
-		}
+	if err := mergePR(ctx, client, defaultOwner, repo, prNumber); err != nil {
+		return fmt.Errorf("merge PR: %w", err)
+	}
 
-		pollInterval := cfg.PRMergePollInterval
-		if envInterval := os.Getenv(configs.PRMergePollInterval); envInterval != "" {
-			if parsed, err := parseIntWithDefault(envInterval, pollInterval); err == nil {
-				pollInterval = parsed
-			}
-		}
+	if err := deleteBranchIfExists(ctx, client, defaultOwner, repo, &github.Reference{Ref: github.Ptr("refs/heads/" + tempBranch)}); err != nil {
+		LogWarning("Failed to delete temp branch after merge", "error", err)
+	}
+	return nil
+}
 
-		var mergeable *bool
-		var mergeableState string
-		owner, repoName := parseRepoPath(key.RepoName)
-		for i := 0; i < maxAttempts; i++ {
-			current, _, gerr := client.PullRequests.Get(ctx, owner, repoName, pr.GetNumber())
-			if gerr == nil && current != nil {
-				mergeable = current.Mergeable
-				mergeableState = current.GetMergeableState()
-				if mergeable != nil { // computed
-					break
-				}
+// pollMergeability polls the GitHub API until the PR's mergeability is computed or attempts are exhausted.
+func pollMergeability(ctx context.Context, client *github.Client, owner string, repo string, prNumber int, maxAttempts int, pollIntervalMs int) (mergeable *bool, state string) {
+	for i := 0; i < maxAttempts; i++ {
+		current, _, err := client.PullRequests.Get(ctx, owner, repo, prNumber)
+		if err == nil && current != nil {
+			mergeable = current.Mergeable
+			state = current.GetMergeableState()
+			if mergeable != nil {
+				return
 			}
-			time.Sleep(time.Duration(pollInterval) * time.Millisecond)
-		}
-		if mergeable != nil && !*mergeable || strings.EqualFold(mergeableState, "dirty") {
-			LogWarning(fmt.Sprintf("PR #%d is not mergeable (state=%s). Likely merge conflicts. Leaving PR open for manual resolution.", pr.GetNumber(), mergeableState))
-			return fmt.Errorf("pull request #%d has merge conflicts (state=%s)", pr.GetNumber(), mergeableState)
 		}
-		if err = mergePR(ctx, client, key.RepoName, pr.GetNumber()); err != nil {
-			return fmt.Errorf("merge PR: %w", err)
-		}
-		if err = deleteBranchIfExists(ctx, client, key.RepoName, &github.Reference{Ref: github.String("refs/heads/" + tempBranch)}); err != nil {
-			// Log but don't fail - branch cleanup is not critical
-			LogWarning(fmt.Sprintf("Failed to delete temp branch after merge: %v", err))
-		}
-	} else {
-		LogInfo(fmt.Sprintf("PR created and awaiting review: #%d", pr.GetNumber()))
+		time.Sleep(time.Duration(pollIntervalMs) * time.Millisecond)
 	}
-	return nil
+	return
 }
 
 // addFilesToBranch builds a tree, creates a commit, and updates the ref (direct to target branch)
-func addFilesToBranch(ctx context.Context, client *github.Client, key UploadKey,
+func addFilesToBranch(ctx context.Context, config *configs.Config, client *github.Client, key types.UploadKey,
 	files []github.RepositoryContent, message string) error {
 
 	entries := make(map[string]string, len(files))
 	for _, f := range files {
-		content, _ := f.GetContent()
+		content, err := f.GetContent()
+		if err != nil {
+			return fmt.Errorf("decode content for %s: %w", f.GetName(), err)
+		}
 		entries[f.GetName()] = content
 	}
 
-	treeSHA, baseSHA, err := createCommitTree(ctx, client, key, entries)
+	treeSHA, baseSHA, err := createCommitTree(ctx, config, client, key, entries)
 	if err != nil {
-		LogCritical(fmt.Sprintf("Error creating commit tree: %v\n", err))
+		LogCritical("Error creating commit tree", "error", err)
 		return err
 	}
-	if err := createCommit(ctx, client, key, baseSHA, treeSHA, message); err != nil {
-		LogCritical(fmt.Sprintf("Error creating commit: %v\n", err))
+	if err := createCommit(ctx, client, config.ConfigRepoOwner, key, baseSHA, treeSHA, message); err != nil {
+		LogCritical("Error creating commit", "error", err)
 		return err
 	}
 	return nil
 }
 
 // createBranch creates a new branch from the specified base branch (defaults to 'main') and deletes it first if it already exists.
-func createBranch(ctx context.Context, client *github.Client, repo, newBranch string, baseBranch ...string) (*github.Reference, error) {
+func createBranch(ctx context.Context, client *github.Client, defaultOwner, repo, newBranch string, baseBranch ...string) (*github.Reference, error) {
 	// Normalize repo name for consistent logging and operations
-	normalizedRepo := normalizeRepoName(repo)
-	owner, repoName := parseRepoPath(normalizedRepo)
+	normalizedRepo := normalizeRepoName(repo, defaultOwner)
+	owner, repoName := parseRepoPath(normalizedRepo, defaultOwner)
 
 	// Use provided base branch or default to "main"
 	base := "main"
@@ -284,75 +309,60 @@ func createBranch(ctx context.Context, client *github.Client, repo, newBranch st
 
 	baseRef, _, err := client.Git.GetRef(ctx, owner, repoName, "refs/heads/"+base)
 	if err != nil {
-		LogCritical(fmt.Sprintf("Failed to get '%s' baseRef: %s", base, err))
+		LogCritical("Failed to get baseRef", "base", base, "error", err)
 		return nil, err
 	}
 
-	// *** Check if branch (newBranchRef) already exists and delete it ***
-	newBranchRef, _, _ := client.Git.GetRef(ctx, owner, repoName, fmt.Sprintf("%s%s", "refs/heads/", newBranch))
-	if err := deleteBranchIfExists(ctx, client, normalizedRepo, newBranchRef); err != nil {
+	// Check if branch already exists and delete it (404 is expected when it doesn't exist)
+	newBranchRef, _, _ := client.Git.GetRef(ctx, owner, repoName, fmt.Sprintf("%s%s", "refs/heads/", newBranch)) //nolint:errcheck // 404 expected
+	if err := deleteBranchIfExists(ctx, client, defaultOwner, normalizedRepo, newBranchRef); err != nil {
 		return nil, fmt.Errorf("failed to delete existing branch %s: %w", newBranch, err)
 	}
 
-	newRef := &github.Reference{
-		Ref: github.String(fmt.Sprintf("%s%s", "refs/heads/", newBranch)),
-		Object: &github.GitObject{
-			SHA: baseRef.Object.SHA,
-		},
+	createRef := github.CreateRef{
+		Ref: fmt.Sprintf("refs/heads/%s", newBranch),
+		SHA: baseRef.Object.GetSHA(),
 	}
 
-	newBranchRef, _, err = client.Git.CreateRef(ctx, owner, repoName, newRef)
+	newBranchRef, _, err = client.Git.CreateRef(ctx, owner, repoName, createRef)
 	if err != nil {
-		LogCritical(fmt.Sprintf("Failed to create newBranchRef %s:  %s", newRef, err))
+		LogCritical("Failed to create newBranchRef", "ref", createRef.Ref, "error", err)
 		return nil, err
 	}
 
-	LogInfo(fmt.Sprintf("Branch created successfully: %s on %s (from %s)", newRef, normalizedRepo, base))
+	LogInfo("Branch created successfully", "ref", createRef.Ref, "repo", normalizedRepo, "base", base)
 
 	return newBranchRef, nil
 }
 
 // createCommitTree looks up the branch ref once, then builds a tree on top of that base commit.
-func createCommitTree(ctx context.Context, client *github.Client, targetBranch UploadKey,
+func createCommitTree(ctx context.Context, config *configs.Config, client *github.Client, targetBranch types.UploadKey,
 	files map[string]string) (treeSHA string, baseSHA string, err error) {
 
+	defaultOwner := config.ConfigRepoOwner
 	// Normalize repo name for consistent logging
-	normalizedRepo := normalizeRepoName(targetBranch.RepoName)
-	owner, repoName := parseRepoPath(normalizedRepo)
-	LogInfo(fmt.Sprintf("DEBUG createCommitTree: targetBranch.RepoName=%q, normalized=%q, parsed owner=%q, repoName=%q",
-		targetBranch.RepoName, normalizedRepo, owner, repoName))
+	normalizedRepo := normalizeRepoName(targetBranch.RepoName, defaultOwner)
+	owner, repoName := parseRepoPath(normalizedRepo, defaultOwner)
+	LogInfo("DEBUG createCommitTree", "target_repo_name", targetBranch.RepoName, "normalized", normalizedRepo, "owner", owner, "repo_name", repoName)
 
 	// 1) Get current ref with retry logic to handle GitHub API eventual consistency
 	// When a branch is just created, it may take a moment to be visible
 	var ref *github.Reference
 
-	// Get retry configuration from environment or use defaults
-	cfg := configs.NewConfig()
-	maxRetries := cfg.GitHubAPIMaxRetries
-	if envRetries := os.Getenv(configs.GitHubAPIMaxRetries); envRetries != "" {
-		if parsed, err := parseIntWithDefault(envRetries, maxRetries); err == nil {
-			maxRetries = parsed
-		}
-	}
-
-	initialRetryDelay := cfg.GitHubAPIInitialRetryDelay
-	if envDelay := os.Getenv(configs.GitHubAPIInitialRetryDelay); envDelay != "" {
-		if parsed, err := parseIntWithDefault(envDelay, initialRetryDelay); err == nil {
-			initialRetryDelay = parsed
-		}
-	}
+	maxRetries := config.GitHubAPIMaxRetries
+	retryDelay := time.Duration(config.GitHubAPIInitialRetryDelay) * time.Millisecond
 
-	retryDelay := time.Duration(initialRetryDelay) * time.Millisecond
+	// GetRef expects "heads/main" format (no "refs/" prefix)
+	refPath := normalizeRefPath(targetBranch.BranchPath, false)
 
 	for attempt := 1; attempt <= maxRetries; attempt++ {
-		ref, _, err = client.Git.GetRef(ctx, owner, repoName, targetBranch.BranchPath)
+		ref, _, err = client.Git.GetRef(ctx, owner, repoName, refPath)
 		if err == nil && ref != nil {
 			break // Success
 		}
 
 		if attempt < maxRetries {
-			LogWarning(fmt.Sprintf("Failed to get ref for %s (attempt %d/%d): %v. Retrying in %v...",
-				normalizedRepo, attempt, maxRetries, err, retryDelay))
+			LogWarning("Failed to get ref; retrying", "repo", normalizedRepo, "attempt", attempt, "max_retries", maxRetries, "error", err, "retry_delay", retryDelay)
 			time.Sleep(retryDelay)
 			retryDelay *= 2 // Exponential backoff
 		}
@@ -360,9 +370,9 @@ func createCommitTree(ctx context.Context, client *github.Client, targetBranch U
 
 	if err != nil || ref == nil {
 		if err == nil {
-			err = errors.Errorf("targetRef is nil after %d attempts", maxRetries)
+			err = fmt.Errorf("targetRef is nil after %d attempts", maxRetries)
 		}
-		LogCritical(fmt.Sprintf("Failed to get ref for %s after %d attempts: %v\n", normalizedRepo, maxRetries, err))
+		LogCritical("Failed to get ref after max attempts", "repo", normalizedRepo, "attempts", maxRetries, "error", err)
 		return "", "", err
 	}
 	baseSHA = ref.GetObject().GetSHA()
@@ -371,10 +381,10 @@ func createCommitTree(ctx context.Context, client *github.Client, targetBranch U
 	var treeEntries []*github.TreeEntry
 	for path, content := range files {
 		treeEntries = append(treeEntries, &github.TreeEntry{
-			Path:    github.String(path),
-			Type:    github.String("blob"),
-			Mode:    github.String("100644"),
-			Content: github.String(content),
+			Path:    github.Ptr(path),
+			Type:    github.Ptr("blob"),
+			Mode:    github.Ptr("100644"),
+			Content: github.Ptr(content),
 		})
 	}
 
@@ -387,33 +397,36 @@ func createCommitTree(ctx context.Context, client *github.Client, targetBranch U
 }
 
 // createCommit makes the commit using the provided baseSHA, and updates the branch ref to the new commit.
-func createCommit(ctx context.Context, client *github.Client, targetBranch UploadKey,
+func createCommit(ctx context.Context, client *github.Client, defaultOwner string, targetBranch types.UploadKey,
 	baseSHA string, treeSHA string, message string) error {
 
-	owner, repoName := parseRepoPath(targetBranch.RepoName)
+	owner, repoName := parseRepoPath(targetBranch.RepoName, defaultOwner)
 
-	parent := &github.Commit{SHA: github.String(baseSHA)}
-	commit := &github.Commit{
-		Message: github.String(message),
-		Tree:    &github.Tree{SHA: github.String(treeSHA)},
+	parent := &github.Commit{SHA: github.Ptr(baseSHA)}
+	commit := github.Commit{
+		Message: github.Ptr(message),
+		Tree:    &github.Tree{SHA: github.Ptr(treeSHA)},
 		Parents: []*github.Commit{parent},
 	}
 
-	newCommit, _, err := client.Git.CreateCommit(ctx, owner, repoName, commit)
+	newCommit, _, err := client.Git.CreateCommit(ctx, owner, repoName, commit, nil)
 	if err != nil {
 		return fmt.Errorf("could not create commit: %w", err)
 	}
 
 	// Update branch ref directly (no second GET)
-	ref := &github.Reference{
-		Ref:    github.String(targetBranch.BranchPath), // e.g., "refs/heads/main"
-		Object: &github.GitObject{SHA: github.String(newCommit.GetSHA())},
-	}
-	if _, _, err := client.Git.UpdateRef(ctx, owner, repoName, ref, false); err != nil {
+	// UpdateRef expects ref path like "heads/main" (without "refs/" prefix)
+	fullRefPath := normalizeRefPath(targetBranch.BranchPath, true)
+	refPath := strings.TrimPrefix(fullRefPath, "refs/")
+	updateRef := github.UpdateRef{
+		SHA:   newCommit.GetSHA(),
+		Force: github.Ptr(false),
+	}
+	if _, _, err := client.Git.UpdateRef(ctx, owner, repoName, refPath, updateRef); err != nil {
 		// Detect non-fast-forward / conflict scenarios and provide a clearer error
 		if eresp, ok := err.(*github.ErrorResponse); ok {
 			if eresp.Response != nil && eresp.Response.StatusCode == http.StatusUnprocessableEntity {
-				return fmt.Errorf("failed to update ref: non-fast-forward (possible conflict). Consider using PR strategy: %w", err)
+				return fmt.Errorf("%w: failed to update ref: non-fast-forward. Consider using PR strategy: %v", ErrMergeConflict, err)
 			}
 		}
 		return fmt.Errorf("failed to update ref to new commit: %w", err)
@@ -422,50 +435,50 @@ func createCommit(ctx context.Context, client *github.Client, targetBranch Uploa
 }
 
 // mergePR merges the specified pull request in the given repository.
-func mergePR(ctx context.Context, client *github.Client, repo string, pr_number int) error {
-	owner, repoName := parseRepoPath(repo)
+func mergePR(ctx context.Context, client *github.Client, defaultOwner, repo string, pr_number int) error {
+	owner, repoName := parseRepoPath(repo, defaultOwner)
 
 	options := &github.PullRequestOptions{
 		MergeMethod: "merge", // Other options: "squash" or "rebase"
 	}
 	result, _, err := client.PullRequests.Merge(ctx, owner, repoName, pr_number, "Merging the pull request", options)
 	if err != nil {
-		LogCritical(fmt.Sprintf("Failed to merge PR: %v\n", err))
+		LogCritical("Failed to merge PR", "error", err)
 		return err
 	}
 	if result.GetMerged() {
-		LogInfo(fmt.Sprintf("Successfully merged PR #%d\n", pr_number))
+		LogInfo("Successfully merged PR", "pr_number", pr_number)
 		return nil
 	} else {
-		LogError(fmt.Sprintf("Failed to merge PR #%d: %s", pr_number, result.GetMessage()))
+		LogError("Failed to merge PR", "pr_number", pr_number, "message", result.GetMessage())
 		return fmt.Errorf("failed to merge PR #%d: %s", pr_number, result.GetMessage())
 	}
 }
 
 // deleteBranchIfExists deletes the specified branch if it exists, except for 'main'.
 // Returns an error if attempting to delete the main branch or if deletion fails.
-func deleteBranchIfExists(backgroundContext context.Context, client *github.Client, repo string, ref *github.Reference) error {
+func deleteBranchIfExists(backgroundContext context.Context, client *github.Client, defaultOwner, repo string, ref *github.Reference) error {
 	// Early return if ref is nil (branch doesn't exist)
 	if ref == nil {
 		return nil
 	}
 
 	// Normalize repo name for consistent logging
-	normalizedRepo := normalizeRepoName(repo)
-	owner, repoName := parseRepoPath(normalizedRepo)
+	normalizedRepo := normalizeRepoName(repo, defaultOwner)
+	owner, repoName := parseRepoPath(normalizedRepo, defaultOwner)
 
 	if ref.GetRef() == "refs/heads/main" {
 		LogError("I refuse to delete branch 'main'.")
 		return fmt.Errorf("refusing to delete protected branch 'main'")
 	}
 
-	LogInfo(fmt.Sprintf("Deleting branch %s on %s", ref.GetRef(), normalizedRepo))
+	LogInfo("Deleting branch", "ref", ref.GetRef(), "repo", normalizedRepo)
 	_, _, err := client.Git.GetRef(backgroundContext, owner, repoName, ref.GetRef())
 
 	if err == nil { // Branch exists (there was no error fetching it)
 		_, err = client.Git.DeleteRef(backgroundContext, owner, repoName, ref.GetRef())
 		if err != nil {
-			LogCritical(fmt.Sprintf("Error deleting branch: %v\n", err))
+			LogCritical("Error deleting branch", "error", err)
 			return fmt.Errorf("failed to delete branch %s: %w", ref.GetRef(), err)
 		}
 	}
@@ -473,15 +486,6 @@ func deleteBranchIfExists(backgroundContext context.Context, client *github.Clie
 }
 
 // DeleteBranchIfExistsExported is an exported wrapper for testing deleteBranchIfExists
-func DeleteBranchIfExistsExported(ctx context.Context, client *github.Client, repo string, ref *github.Reference) error {
-	return deleteBranchIfExists(ctx, client, repo, ref)
-}
-
-// parseIntWithDefault parses a string to int, returning defaultValue on error
-func parseIntWithDefault(s string, defaultValue int) (int, error) {
-	var result int
-	if _, err := fmt.Sscanf(s, "%d", &result); err != nil {
-		return defaultValue, err
-	}
-	return result, nil
+func DeleteBranchIfExistsExported(ctx context.Context, client *github.Client, defaultOwner, repo string, ref *github.Reference) error {
+	return deleteBranchIfExists(ctx, client, defaultOwner, repo, ref)
 }
diff --git a/services/github_write_to_target_test.go b/services/github_write_to_target_test.go
index a645836..57c53e3 100644
--- a/services/github_write_to_target_test.go
+++ b/services/github_write_to_target_test.go
@@ -14,248 +14,80 @@ import (
 	"strings"
 	"testing"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/configs"
 	"github.com/grove-platform/github-copier/services"
 	"github.com/grove-platform/github-copier/types"
 	"github.com/jarcoal/httpmock"
 	"github.com/stretchr/testify/require"
 
-	// test helpers (utils.go)
 	test "github.com/grove-platform/github-copier/tests"
 )
 
 func TestMain(m *testing.M) {
-	// Minimal env so init() and any env readers are happy.
-	os.Setenv(configs.ConfigRepoOwner, "my-org")
-	os.Setenv(configs.ConfigRepoName, "config-repo")
-	os.Setenv(configs.InstallationId, "12345")
-	os.Setenv(configs.AppId, "1166559")
-	os.Setenv(configs.AppClientId, "IvTestClientId")
-	os.Setenv("SKIP_SECRET_MANAGER", "true")
-	os.Setenv(configs.ConfigRepoBranch, "main")
-
-	// Provide an RSA private key (both raw and b64) so ConfigurePermissions can parse.
+	_ = os.Setenv(configs.ConfigRepoOwner, "my-org")
+	_ = os.Setenv(configs.ConfigRepoName, "config-repo")
+	_ = os.Setenv(configs.InstallationId, "12345")
+	_ = os.Setenv(configs.AppId, "1166559")
+	_ = os.Setenv(configs.AppClientId, "IvTestClientId")
+	_ = os.Setenv("SKIP_SECRET_MANAGER", "true")
+	_ = os.Setenv(configs.ConfigRepoBranch, "main")
+
 	key, _ := rsa.GenerateKey(rand.Reader, 1024)
 	der := x509.MarshalPKCS1PrivateKey(key)
 	pemBytes := pem.EncodeToMemory(&pem.Block{Type: "RSA PRIVATE KEY", Bytes: der})
-	os.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
-	os.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
+	_ = os.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
+	_ = os.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
 
 	code := m.Run()
 
-	// Cleanup
-	os.Unsetenv(configs.ConfigRepoOwner)
-	os.Unsetenv(configs.ConfigRepoName)
-	os.Unsetenv(configs.InstallationId)
-	os.Unsetenv(configs.AppId)
-	os.Unsetenv(configs.AppClientId)
-	os.Unsetenv("SKIP_SECRET_MANAGER")
-	os.Unsetenv("SRC_BRANCH")
-	os.Unsetenv("GITHUB_APP_PRIVATE_KEY")
-	os.Unsetenv("GITHUB_APP_PRIVATE_KEY_B64")
+	_ = os.Unsetenv(configs.ConfigRepoOwner)
+	_ = os.Unsetenv(configs.ConfigRepoName)
+	_ = os.Unsetenv(configs.InstallationId)
+	_ = os.Unsetenv(configs.AppId)
+	_ = os.Unsetenv(configs.AppClientId)
+	_ = os.Unsetenv("SKIP_SECRET_MANAGER")
+	_ = os.Unsetenv("SRC_BRANCH")
+	_ = os.Unsetenv("GITHUB_APP_PRIVATE_KEY")
+	_ = os.Unsetenv("GITHUB_APP_PRIVATE_KEY_B64")
 
 	os.Exit(code)
 }
 
-// LEGACY TESTS - These tests are for legacy code that was removed in commit a64726c
-// The AddToRepoAndFilesMap and IterateFilesForCopy functions were removed as part of the
-// migration to the new pattern-matching system. These tests are commented out but kept for reference.
-//
-// The new system uses pattern matching rules defined in YAML config files.
-// See pattern_matcher_test.go for tests of the new system.
-
-/*
-func TestAddToRepoAndFilesMap_NewEntry(t *testing.T) {
-	services.FilesToUpload = nil
-
-	name := "example.txt"
-	dummyFile := github.RepositoryContent{Name: &name}
-
-	services.AddToRepoAndFilesMap("TargetRepo1", "main", dummyFile)
-
-	require.NotNil(t, services.FilesToUpload, "FilesToUpload map should be initialized")
-	key := types.UploadKey{RepoName: "TargetRepo1", BranchPath: "refs/heads/main", RuleName: "", CommitStrategy: ""}
-	entry, exists := services.FilesToUpload[key]
-	require.True(t, exists, "Entry for TargetRepo1/main should exist")
-	require.Equal(t, "main", entry.TargetBranch)
-	require.Len(t, entry.Content, 1)
-	require.Equal(t, "example.txt", *entry.Content[0].Name)
-}
-
-func TestAddToRepoAndFilesMap_AppendEntry(t *testing.T) {
-	services.FilesToUpload = make(map[types.UploadKey]types.UploadFileContent)
-	key := types.UploadKey{RepoName: "TargetRepo1", BranchPath: "refs/heads/main", RuleName: "", CommitStrategy: ""}
-
-	initialName := "first.txt"
-	services.FilesToUpload[key] = types.UploadFileContent{
-		TargetBranch: "main",
-		Content:      []github.RepositoryContent{{Name: &initialName}},
-	}
-
-	newName := "second.txt"
-	newFile := github.RepositoryContent{Name: &newName}
-	services.AddToRepoAndFilesMap("TargetRepo1", "main", newFile)
-
-	entry := services.FilesToUpload[key]
-	require.Len(t, entry.Content, 2)
-	require.ElementsMatch(t, []string{"first.txt", "second.txt"},
-		[]string{*entry.Content[0].Name, *entry.Content[1].Name})
-}
-
-func TestAddToRepoAndFilesMap_NestedFiles(t *testing.T) {
-	services.FilesToUpload = make(map[types.UploadKey]types.UploadFileContent)
-	key := types.UploadKey{RepoName: "TargetRepo1", BranchPath: "refs/heads/main", RuleName: "", CommitStrategy: ""}
-
-	initialName := "level1/first.txt"
-	services.FilesToUpload[key] = types.UploadFileContent{
-		TargetBranch: "main",
-		Content:      []github.RepositoryContent{{Name: &initialName}},
-	}
-
-	newName := "level1/level2/level3/nested-second.txt"
-	newFile := github.RepositoryContent{Name: &newName}
-	services.AddToRepoAndFilesMap("TargetRepo1", "main", newFile)
-
-	entry := services.FilesToUpload[key]
-	require.Len(t, entry.Content, 2)
-	require.ElementsMatch(t, []string{"level1/first.txt", "level1/level2/level3/nested-second.txt"},
-		[]string{*entry.Content[0].Name, *entry.Content[1].Name})
-}
-
-func TestIterateFilesForCopy_Deletes(t *testing.T) {
-	cfg := types.Configs{
-		SourceDirectory: "src/examples",
-		TargetRepo:      "TargetRepo1",
-		TargetBranch:    "main",
-		TargetDirectory: "dest/examples",
-		RecursiveCopy:   false,
-	}
-	configFile := types.ConfigFileType{cfg}
-	changed := []types.ChangedFile{{
-		Path:   "src/examples/sample.txt",
-		Status: "DELETED",
-	}}
-
-	services.FilesToUpload = nil
-	services.FilesToDeprecate = nil
-
-	err := services.IterateFilesForCopy(changed, configFile)
-	require.NoError(t, err)
-
-	targetPath := "dest/examples/sample.txt"
-	require.Contains(t, services.FilesToDeprecate, targetPath)
-	require.Equal(t, cfg, services.FilesToDeprecate[targetPath])
-	require.Nil(t, services.FilesToUpload)
-}
-
-func TestIterateFilesForCopy_RecursiveVsNonRecursive(t *testing.T) {
-	t.Setenv("SRC_BRANCH", "main")
-	_ = test.WithHTTPMock(t)
-
-	owner, repo := test.EnvOwnerRepo(t)
-
-	// Simulate changes under the source directory
-	changed := []types.ChangedFile{
-		test.MakeChanged("ADDED", "examples/a.txt"),
-		test.MakeChanged("MODIFIED", "examples/sub/b.txt"),
-		test.MakeChanged("ADDED", "examples/sub/deeper/c.txt"),
-	}
-
-	// Helper to base64-encode small content blobs
-	b64 := func(s string) string { return base64.StdEncoding.EncodeToString([]byte(s)) }
-
-	// Register responders for owner/repo
-	for _, or := range [][2]string{{owner, repo}, {"REPO_OWNER", "REPO_NAME"}} {
-		test.MockContentsEndpoint(or[0], or[1], "examples/a.txt", b64("A"))
-		test.MockContentsEndpoint(or[0], or[1], "examples/sub/b.txt", b64("B"))
-		test.MockContentsEndpoint(or[0], or[1], "examples/sub/deeper/c.txt", b64("C"))
-	}
-
-	// Same source; two configs exercising recursive vs non-recursive and different targets
-	cases := []struct {
-		name   string
-		cfg    types.Configs
-		expect []string // expected TARGET paths
-	}{
-		{
-			name: "recursive=true copies all depths",
-			cfg: types.Configs{
-				SourceDirectory: "examples",
-				TargetRepo:      "TargetRepoR",
-				TargetBranch:    "main",
-				TargetDirectory: "dest",
-				RecursiveCopy:   true,
-			},
-			expect: []string{
-				"dest/a.txt",
-				"dest/sub/b.txt",
-				"dest/sub/deeper/c.txt",
-			},
-		},
-		{
-			name: "recursive=false copies only root files",
-			cfg: types.Configs{
-				SourceDirectory: "examples",
-				TargetRepo:      "TargetRepoNR",
-				TargetBranch:    "main",
-				TargetDirectory: "dest",
-				RecursiveCopy:   false,
-			},
-			expect: []string{
-				"dest/a.txt",
-			},
-		},
-	}
-
-	for _, tc := range cases {
-		t.Run(tc.name, func(t *testing.T) {
-			test.ResetGlobals()
-			err := services.IterateFilesForCopy(changed, types.ConfigFileType{tc.cfg})
-			require.NoError(t, err)
-			// Compares staged entries cfg.SourceDirectory -> cfg.TargetDirectory.
-			test.AssertUploadedPathsFromConfig(t, tc.cfg, tc.expect)
-		})
-	}
-}
-*/
-
-func TestAddFilesToTargetRepoBranch_Succeeds(t *testing.T) {
+func TestAddFilesToTargetRepos_Direct_Succeeds(t *testing.T) {
 	_ = test.WithHTTPMock(t)
 
 	owner, repo := test.EnvOwnerRepo(t)
 	branch := "main"
 
-	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
 
 	baseRefURL, commitsURL, updateRefURL := test.MockGitHubWriteEndpoints(owner, repo, branch)
 
 	files := []github.RepositoryContent{
 		{
-			Name:    github.String("dir/example1.txt"),
-			Path:    github.String("dir/example1.txt"),
-			Content: github.String(base64.StdEncoding.EncodeToString([]byte("hello 1"))),
+			Name:    github.Ptr("dir/example1.txt"),
+			Path:    github.Ptr("dir/example1.txt"),
+			Content: github.Ptr(base64.StdEncoding.EncodeToString([]byte("hello 1"))),
 		},
 		{
-			Name:    github.String("dir/example2.txt"),
-			Path:    github.String("dir/example2.txt"),
-			Content: github.String(base64.StdEncoding.EncodeToString([]byte("hello 2"))),
+			Name:    github.Ptr("dir/example2.txt"),
+			Path:    github.Ptr("dir/example2.txt"),
+			Content: github.Ptr(base64.StdEncoding.EncodeToString([]byte("hello 2"))),
 		},
 	}
-	services.FilesToUpload = map[types.UploadKey]types.UploadFileContent{
+	filesToUpload := map[types.UploadKey]types.UploadFileContent{
 		{RepoName: repo, BranchPath: "refs/heads/" + branch}: {
 			TargetBranch: branch,
 			Content:      files,
 		},
 	}
 
-	services.AddFilesToTargetRepoBranch()
+	services.AddFilesToTargetRepos(context.Background(), test.TestConfig(), filesToUpload, nil, nil)
 
 	info := httpmock.GetCallCountInfo()
 	require.Equal(t, 1, info["GET "+baseRefURL])
 
-	// POST /git/trees is registered via regex; sum by prefix
 	treeCalls := 0
 	for k, v := range info {
 		if strings.HasPrefix(k, "POST https://api.github.com/repos/"+owner+"/"+repo+"/git/trees") {
@@ -263,27 +95,24 @@ func TestAddFilesToTargetRepoBranch_Succeeds(t *testing.T) {
 		}
 	}
 	require.Equal(t, 1, treeCalls)
-
 	require.Equal(t, 1, info["POST "+commitsURL])
 	require.Equal(t, 1, info["PATCH "+updateRefURL])
-
-	services.FilesToUpload = nil
 }
 
-func TestAddFilesToTargetRepoBranch_ViaPR_Succeeds(t *testing.T) {
+func TestAddFilesToTargetRepos_ViaPR_Succeeds(t *testing.T) {
 	_ = test.WithHTTPMock(t)
 	t.Setenv("COPIER_COMMIT_STRATEGY", "pr")
 
 	owner, repo := test.EnvOwnerRepo(t)
 	baseBranch := "main"
 
-	// Force fresh token; stub token endpoint then configure permissions.
-	services.InstallationAccessToken = ""
-	test.MockGitHubAppTokenEndpoint(os.Getenv(configs.InstallationId))
-	err := services.ConfigurePermissions()
+	// Force fresh token
+	services.DefaultTokenManager().SetInstallationAccessToken("")
+	cfg := test.TestConfig()
+	test.MockGitHubAppTokenEndpoint(cfg.InstallationId)
+	err := services.ConfigurePermissions(context.Background(), cfg)
 	require.NoError(t, err, "ConfigurePermissions should succeed")
 
-	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
 
 	// Base ref used to create temp branch
@@ -294,10 +123,8 @@ func TestAddFilesToTargetRepoBranch_ViaPR_Succeeds(t *testing.T) {
 		}),
 	)
 
-	// Create temp branch
 	createRefURL := test.MockCreateRef(owner, repo)
 
-	// Temp branch: GET ref, POST tree, POST commit, PATCH ref
 	tempHead := `copier/\d{8}-\d{6}`
 	httpmock.RegisterRegexpResponder("GET",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/ref/(?:refs/)?heads/`+tempHead+`$`),
@@ -318,24 +145,22 @@ func TestAddFilesToTargetRepoBranch_ViaPR_Succeeds(t *testing.T) {
 		httpmock.NewStringResponder(200, "{}"),
 	)
 
-	// PR create + merge; delete temp branch
 	test.MockPullsAndMerge(owner, repo, 42)
 	test.MockDeleteTempRef(owner, repo)
 
-	// Stage files to baseBranch; service will write via temp branch → PR merge
 	files := []github.RepositoryContent{
 		{
-			Name:    github.String("dir/example1.txt"),
-			Path:    github.String("dir/example1.txt"),
-			Content: github.String(base64.StdEncoding.EncodeToString([]byte("hello 1"))),
+			Name:    github.Ptr("dir/example1.txt"),
+			Path:    github.Ptr("dir/example1.txt"),
+			Content: github.Ptr(base64.StdEncoding.EncodeToString([]byte("hello 1"))),
 		},
 		{
-			Name:    github.String("dir/example2.txt"),
-			Path:    github.String("dir/example2.txt"),
-			Content: github.String(base64.StdEncoding.EncodeToString([]byte("hello 2"))),
+			Name:    github.Ptr("dir/example2.txt"),
+			Path:    github.Ptr("dir/example2.txt"),
+			Content: github.Ptr(base64.StdEncoding.EncodeToString([]byte("hello 2"))),
 		},
 	}
-	services.FilesToUpload = map[types.UploadKey]types.UploadFileContent{
+	filesToUpload := map[types.UploadKey]types.UploadFileContent{
 		{RepoName: repo, BranchPath: "refs/heads/" + baseBranch}: {
 			TargetBranch:   baseBranch,
 			Content:        files,
@@ -344,11 +169,10 @@ func TestAddFilesToTargetRepoBranch_ViaPR_Succeeds(t *testing.T) {
 		},
 	}
 
-	services.AddFilesToTargetRepoBranch()
+	services.AddFilesToTargetRepos(context.Background(), cfg, filesToUpload, nil, nil)
 
-	// Assertions
 	require.Equal(t, 1, test.CountByMethodAndURLRegexp("POST",
-		regexp.MustCompile(`/app/installations/`+regexp.QuoteMeta(os.Getenv(configs.InstallationId))+`/access_tokens$`),
+		regexp.MustCompile(`/app/installations/`+regexp.QuoteMeta(cfg.InstallationId)+`/access_tokens$`),
 	))
 	info := httpmock.GetCallCountInfo()
 	require.Equal(t, 1, info["POST "+createRefURL])
@@ -386,22 +210,16 @@ func TestAddFilesToTargetRepoBranch_ViaPR_Succeeds(t *testing.T) {
 			regexp.MustCompile(`/repos/`+regexp.QuoteMeta(owner)+`/`+regexp.QuoteMeta(repo)+`/git/refs/heads/copier/\d{8}-\d{6}$`)),
 		1,
 	)
-
-	services.FilesToUpload = nil
 }
 
-// --- Added critical tests for merge conflicts and configuration/default priorities ---
-
 func TestAddFiles_DirectConflict_NonFastForward(t *testing.T) {
 	_ = test.WithHTTPMock(t)
 
 	owner, repo := test.EnvOwnerRepo(t)
 	branch := "main"
 
-	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
 
-	// Mock standard direct write endpoints
 	baseRefURL, commitsURL, updateRefURL := test.MockGitHubWriteEndpoints(owner, repo, branch)
 
 	// Override UpdateRef to simulate 422 Unprocessable Entity (non-fast-forward)
@@ -411,27 +229,24 @@ func TestAddFiles_DirectConflict_NonFastForward(t *testing.T) {
 
 	files := []github.RepositoryContent{
 		{
-			Name:    github.String("dir/example1.txt"),
-			Path:    github.String("dir/example1.txt"),
-			Content: github.String(base64.StdEncoding.EncodeToString([]byte("hello 1"))),
+			Name:    github.Ptr("dir/example1.txt"),
+			Path:    github.Ptr("dir/example1.txt"),
+			Content: github.Ptr(base64.StdEncoding.EncodeToString([]byte("hello 1"))),
 		},
 	}
-	services.FilesToUpload = map[types.UploadKey]types.UploadFileContent{
+	filesToUpload := map[types.UploadKey]types.UploadFileContent{
 		{RepoName: repo, BranchPath: "refs/heads/" + branch}: {
 			TargetBranch: branch,
 			Content:      files,
 		},
 	}
 
-	// Run – should not panic; error is handled/logged internally.
-	services.AddFilesToTargetRepoBranch()
+	services.AddFilesToTargetRepos(context.Background(), test.TestConfig(), filesToUpload, nil, nil)
 
 	info := httpmock.GetCallCountInfo()
 	require.Equal(t, 1, info["GET "+baseRefURL])
 	require.Equal(t, 1, info["POST "+commitsURL])
 	require.Equal(t, 1, info["PATCH "+updateRefURL])
-
-	services.FilesToUpload = nil
 }
 
 func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
@@ -441,16 +256,14 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 	owner, repo := test.EnvOwnerRepo(t)
 	baseBranch := "main"
 
-	// Fresh token path
-	services.InstallationAccessToken = ""
-	test.MockGitHubAppTokenEndpoint(os.Getenv(configs.InstallationId))
-	err := services.ConfigurePermissions()
+	cfg := test.TestConfig()
+	services.DefaultTokenManager().SetInstallationAccessToken("")
+	test.MockGitHubAppTokenEndpoint(cfg.InstallationId)
+	err := services.ConfigurePermissions(context.Background(), cfg)
 	require.NoError(t, err, "ConfigurePermissions should succeed")
 
-	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
 
-	// Base ref for creating temp branch
 	httpmock.RegisterRegexpResponder("GET",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/ref/(?:refs/)?heads/`+baseBranch+`$`),
 		httpmock.NewJsonResponderOrPanic(200, map[string]any{
@@ -459,7 +272,6 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 	)
 	createRefURL := test.MockCreateRef(owner, repo)
 
-	// Temp branch interactions
 	tempHead := `copier/\d{8}-\d{6}`
 	httpmock.RegisterRegexpResponder("GET",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/ref/(?:refs/)?heads/`+tempHead+`$`),
@@ -467,7 +279,6 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 			"ref": "refs/heads/copier/20250101-000000", "object": map[string]any{"sha": "baseSha"},
 		}),
 	)
-	// Mock DELETE for existing temp branch cleanup
 	httpmock.RegisterRegexpResponder("DELETE",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/refs/heads/`+tempHead+`$`),
 		httpmock.NewStringResponder(204, ""),
@@ -485,27 +296,22 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 		httpmock.NewStringResponder(200, "{}"),
 	)
 
-	// PR create
 	pr_number := 77
 	httpmock.RegisterResponder("POST",
 		"https://api.github.com/repos/"+owner+"/"+repo+"/pulls",
 		httpmock.NewJsonResponderOrPanic(201, map[string]any{"number": pr_number, "html_url": "https://github.com/" + owner + "/" + repo + "/pull/77"}),
 	)
-	// PR mergeability check returns dirty -> not mergeable
 	httpmock.RegisterResponder("GET",
 		"https://api.github.com/repos/"+owner+"/"+repo+"/pulls/77",
 		httpmock.NewJsonResponderOrPanic(200, map[string]any{"mergeable": false, "mergeable_state": "dirty"}),
 	)
-	// Note: do NOT register PUT /merge to ensure it isn't called
-	// Also do NOT register DELETE for temp ref; conflict path returns early before cleanup
 
-	// Minimal file to write
 	files := []github.RepositoryContent{{
-		Name:    github.String("f.txt"),
-		Path:    github.String("f.txt"),
-		Content: github.String(base64.StdEncoding.EncodeToString([]byte("x"))),
+		Name:    github.Ptr("f.txt"),
+		Path:    github.Ptr("f.txt"),
+		Content: github.Ptr(base64.StdEncoding.EncodeToString([]byte("x"))),
 	}}
-	services.FilesToUpload = map[types.UploadKey]types.UploadFileContent{
+	filesToUpload := map[types.UploadKey]types.UploadFileContent{
 		{RepoName: repo, BranchPath: "refs/heads/" + baseBranch}: {
 			TargetBranch:   baseBranch,
 			Content:        files,
@@ -513,22 +319,16 @@ func TestAddFiles_ViaPR_MergeConflict_Dirty_NotMerged(t *testing.T) {
 		},
 	}
 
-	services.AddFilesToTargetRepoBranch()
+	services.AddFilesToTargetRepos(context.Background(), cfg, filesToUpload, nil, nil)
 
-	// Assertions
 	info := httpmock.GetCallCountInfo()
 	require.Equal(t, 1, info["POST "+createRefURL])
 	require.Equal(t, 1, test.CountByMethodAndURLRegexp("POST",
 		regexp.MustCompile(`/repos/`+regexp.QuoteMeta(owner)+`/`+regexp.QuoteMeta(repo)+`/pulls$`)))
-	// No merge call should have been made
 	require.Equal(t, 0, test.CountByMethodAndURLRegexp("PUT",
 		regexp.MustCompile(`/repos/`+regexp.QuoteMeta(owner)+`/`+regexp.QuoteMeta(repo)+`/pulls/77/merge$`)))
-	// Only 1 DELETE call for initial cleanup of existing branch (before creating new one)
-	// No additional DELETE after merge conflict because we returned early
 	require.Equal(t, 1, test.CountByMethodAndURLRegexp("DELETE",
 		regexp.MustCompile(`/repos/`+regexp.QuoteMeta(owner)+`/`+regexp.QuoteMeta(repo)+`/git/refs/heads/copier/\d{8}-\d{6}$`)))
-
-	services.FilesToUpload = nil
 }
 
 func TestPriority_Strategy_ConfigOverridesEnv_And_MessageFallbacks(t *testing.T) {
@@ -537,22 +337,18 @@ func TestPriority_Strategy_ConfigOverridesEnv_And_MessageFallbacks(t *testing.T)
 	owner, repo := test.EnvOwnerRepo(t)
 	baseBranch := "main"
 
-	// Env specifies PR, but config will override to direct
 	t.Setenv("COPIER_COMMIT_STRATEGY", "pr")
 
-	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
 
-	// Mocks for direct flow
 	baseRefURL, commitsURL, updateRefURL := test.MockGitHubWriteEndpoints(owner, repo, baseBranch)
 
-	// Intercept POST commit to assert commit message fallback when config empty but env default set
 	wantMsg := "Env Default Commit Message"
-	t.Setenv(configs.DefaultCommitMessage, wantMsg)
+	testCfg := test.TestConfig()
+	testCfg.DefaultCommitMessage = wantMsg
 
-	// Replace commits responder with custom body assertion
 	httpmock.RegisterResponder("POST", commitsURL, func(req *http.Request) (*http.Response, error) {
-		defer req.Body.Close()
+		defer func() { _ = req.Body.Close() }()
 		b, _ := io.ReadAll(req.Body)
 		if !strings.Contains(string(b), wantMsg) {
 			t.Fatalf("commit body does not contain expected message: %s; body=%s", wantMsg, string(b))
@@ -561,32 +357,28 @@ func TestPriority_Strategy_ConfigOverridesEnv_And_MessageFallbacks(t *testing.T)
 	})
 
 	files := []github.RepositoryContent{{
-		Name:    github.String("a.txt"),
-		Path:    github.String("a.txt"),
-		Content: github.String(base64.StdEncoding.EncodeToString([]byte("x"))),
+		Name:    github.Ptr("a.txt"),
+		Path:    github.Ptr("a.txt"),
+		Content: github.Ptr(base64.StdEncoding.EncodeToString([]byte("x"))),
 	}}
 
-	cfg := types.Configs{
+	typeCfg := types.Configs{
 		TargetRepo:           repo,
 		TargetBranch:         baseBranch,
 		CopierCommitStrategy: "direct", // overrides env "pr"
-		// CommitMessage empty -> use env default
 	}
 
-	services.FilesToUpload = map[types.UploadKey]types.UploadFileContent{
-		{RepoName: repo, BranchPath: "refs/heads/" + baseBranch, CommitStrategy: cfg.CopierCommitStrategy}: {TargetBranch: baseBranch, Content: files},
+	filesToUpload := map[types.UploadKey]types.UploadFileContent{
+		{RepoName: repo, BranchPath: "refs/heads/" + baseBranch, CommitStrategy: typeCfg.CopierCommitStrategy}: {TargetBranch: baseBranch, Content: files},
 	}
 
-	services.AddFilesToTargetRepoBranch() // No longer takes parameters - uses FilesToUpload map
+	services.AddFilesToTargetRepos(context.Background(), testCfg, filesToUpload, nil, nil)
 
 	info := httpmock.GetCallCountInfo()
 	require.Equal(t, 1, info["GET "+baseRefURL])
 	require.Equal(t, 1, info["POST "+commitsURL])
 	require.Equal(t, 1, info["PATCH "+updateRefURL])
-	// No PR endpoints should be called
 	require.Equal(t, 0, test.CountByMethodAndURLRegexp("POST", regexp.MustCompile(`/pulls$`)))
-
-	services.FilesToUpload = nil
 }
 
 func TestPriority_PRTitleDefaultsToCommitMessage_And_NoAutoMergeWhenConfigPresent(t *testing.T) {
@@ -596,16 +388,14 @@ func TestPriority_PRTitleDefaultsToCommitMessage_And_NoAutoMergeWhenConfigPresen
 	owner, repo := test.EnvOwnerRepo(t)
 	baseBranch := "main"
 
-	// Token setup
-	services.InstallationAccessToken = ""
-	test.MockGitHubAppTokenEndpoint(os.Getenv(configs.InstallationId))
-	err := services.ConfigurePermissions()
+	cfg := test.TestConfig()
+	services.DefaultTokenManager().SetInstallationAccessToken("")
+	test.MockGitHubAppTokenEndpoint(cfg.InstallationId)
+	err := services.ConfigurePermissions(context.Background(), cfg)
 	require.NoError(t, err, "ConfigurePermissions should succeed")
 
-	// Set up cached token for the org to bypass GitHub App auth
 	test.SetupOrgToken(owner, "test-token")
 
-	// Base ref and temp branch setup
 	httpmock.RegisterRegexpResponder("GET",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/ref/(?:refs/)?heads/`+baseBranch+`$`),
 		httpmock.NewJsonResponderOrPanic(200, map[string]any{"ref": "refs/heads/" + baseBranch, "object": map[string]any{"sha": "baseSha"}}),
@@ -616,7 +406,6 @@ func TestPriority_PRTitleDefaultsToCommitMessage_And_NoAutoMergeWhenConfigPresen
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/ref/(?:refs/)?heads/`+tempHead+`$`),
 		httpmock.NewJsonResponderOrPanic(200, map[string]any{"ref": "refs/heads/copier/20250101-000000", "object": map[string]any{"sha": "baseSha"}}),
 	)
-	// Mock DELETE for existing temp branch cleanup
 	httpmock.RegisterRegexpResponder("DELETE",
 		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+repo+`/git/refs/heads/`+tempHead+`$`),
 		httpmock.NewStringResponder(204, ""),
@@ -627,7 +416,7 @@ func TestPriority_PRTitleDefaultsToCommitMessage_And_NoAutoMergeWhenConfigPresen
 	)
 	commitsURL := "https://api.github.com/repos/" + owner + "/" + repo + "/git/commits"
 	want := "Env Fallback Message"
-	t.Setenv(configs.DefaultCommitMessage, want)
+	cfg.DefaultCommitMessage = want
 	httpmock.RegisterResponder("POST", commitsURL, func(req *http.Request) (*http.Response, error) {
 		b, _ := io.ReadAll(req.Body)
 		if !strings.Contains(string(b), want) {
@@ -640,7 +429,6 @@ func TestPriority_PRTitleDefaultsToCommitMessage_And_NoAutoMergeWhenConfigPresen
 		httpmock.NewStringResponder(200, "{}"),
 	)
 
-	// Assert PR title equals commit message when PRTitle empty
 	httpmock.RegisterResponder("POST",
 		"https://api.github.com/repos/"+owner+"/"+repo+"/pulls",
 		func(req *http.Request) (*http.Response, error) {
@@ -652,44 +440,34 @@ func TestPriority_PRTitleDefaultsToCommitMessage_And_NoAutoMergeWhenConfigPresen
 		},
 	)
 
-	// No merge; MergeWithoutReview=false when matching config present and not set to true
-	// If code attempted merge, there would be a 404 on PUT, failing the test via missing responder count.
-
 	files := []github.RepositoryContent{{
-		Name: github.String("only.txt"), Path: github.String("only.txt"),
-		Content: github.String(base64.StdEncoding.EncodeToString([]byte("y"))),
+		Name: github.Ptr("only.txt"), Path: github.Ptr("only.txt"),
+		Content: github.Ptr(base64.StdEncoding.EncodeToString([]byte("y"))),
 	}}
-	// cfg := types.Configs{TargetRepo: repo, TargetBranch: baseBranch /* MergeWithoutReview: false (zero value) */}
-	services.FilesToUpload = map[types.UploadKey]types.UploadFileContent{{RepoName: repo, BranchPath: "refs/heads/" + baseBranch, RuleName: "", CommitStrategy: "pr"}: {TargetBranch: baseBranch, Content: files, CommitStrategy: "pr"}}
+	filesToUpload := map[types.UploadKey]types.UploadFileContent{
+		{RepoName: repo, BranchPath: "refs/heads/" + baseBranch, RuleName: "", CommitStrategy: "pr"}: {TargetBranch: baseBranch, Content: files, CommitStrategy: "pr"},
+	}
 
-	services.AddFilesToTargetRepoBranch() // No longer takes parameters - uses FilesToUpload map
+	services.AddFilesToTargetRepos(context.Background(), cfg, filesToUpload, nil, nil)
 
-	// Ensure a PR was created but no merge occurred
 	require.Equal(t, 1, test.CountByMethodAndURLRegexp("POST", regexp.MustCompile(`/pulls$`)))
 	require.Equal(t, 0, test.CountByMethodAndURLRegexp("PUT", regexp.MustCompile(`/pulls/5/merge$`)))
-
-	services.FilesToUpload = nil
 }
 
-// TestDeleteBranchIfExists_NilReference tests that deleteBranchIfExists handles nil references gracefully
 func TestDeleteBranchIfExists_NilReference(t *testing.T) {
 	_ = test.WithHTTPMock(t)
 
-	// Force fresh token
-	services.InstallationAccessToken = ""
-	test.MockGitHubAppTokenEndpoint(os.Getenv(configs.InstallationId))
-	err := services.ConfigurePermissions()
+	cfg := test.TestConfig()
+	services.DefaultTokenManager().SetInstallationAccessToken("")
+	test.MockGitHubAppTokenEndpoint(cfg.InstallationId)
+	err := services.ConfigurePermissions(context.Background(), cfg)
 	require.NoError(t, err, "ConfigurePermissions should succeed")
 
-	// This should not panic or make any API calls when ref is nil
-	// We're testing that the function returns early without attempting to delete
 	ctx := context.Background()
 	client := services.GetRestClient()
 
-	// Call with nil reference - should return immediately without error
-	err = services.DeleteBranchIfExistsExported(ctx, client, "test-org/test-repo", nil)
+	err = services.DeleteBranchIfExistsExported(ctx, client, cfg.ConfigRepoOwner, "test-org/test-repo", nil)
 	require.NoError(t, err, "DeleteBranchIfExistsExported should succeed with nil ref")
 
-	// Verify no DELETE requests were made (since ref was nil)
 	require.Equal(t, 0, test.CountByMethodAndURLRegexp("DELETE", regexp.MustCompile(`/git/refs/`)))
 }
diff --git a/services/health_metrics.go b/services/health_metrics.go
index 104e4d2..3f7ff73 100644
--- a/services/health_metrics.go
+++ b/services/health_metrics.go
@@ -1,6 +1,7 @@
 package services
 
 import (
+	"context"
 	"encoding/json"
 	"net/http"
 	"sync"
@@ -217,21 +218,21 @@ func (mc *MetricsCollector) RecordGitHubAPIError() {
 func (mc *MetricsCollector) GetFilesMatched() int {
 	mc.mu.RLock()
 	defer mc.mu.RUnlock()
-	return int(mc.filesMatched)
+	return int(mc.filesMatched) // #nosec G115 -- counter fits in int
 }
 
 // GetFilesUploaded returns the current files uploaded count
 func (mc *MetricsCollector) GetFilesUploaded() int {
 	mc.mu.RLock()
 	defer mc.mu.RUnlock()
-	return int(mc.filesUploaded)
+	return int(mc.filesUploaded) // #nosec G115 -- counter fits in int
 }
 
 // GetFilesUploadFailed returns the current files upload failed count
 func (mc *MetricsCollector) GetFilesUploadFailed() int {
 	mc.mu.RLock()
 	defer mc.mu.RUnlock()
-	return int(mc.filesUploadFailed)
+	return int(mc.filesUploadFailed) // #nosec G115 -- counter fits in int
 }
 
 // GetMetrics returns current metrics
@@ -287,10 +288,7 @@ func (mc *MetricsCollector) GetMetrics(fileStateService FileStateService) Metric
 			Calls:     mc.githubAPICalls,
 			Errors:    mc.githubAPIErrors,
 			ErrorRate: githubErrorRate,
-			RateLimit: RateLimitInfo{
-				Remaining: 5000, // TODO: Get from GitHub API
-				ResetAt:   time.Now().Add(1 * time.Hour),
-			},
+			RateLimit: currentRateLimitInfo(),
 		},
 		Queues: QueueMetrics{
 			UploadQueueSize:      len(uploadQueue),
@@ -341,31 +339,101 @@ func calculateStats(durations []time.Duration) ProcessingTimeStats {
 	}
 }
 
-// HealthHandler handles /health endpoint
-func HealthHandler(fileStateService FileStateService, startTime time.Time) http.HandlerFunc {
+// HealthHandler handles /health (liveness) endpoint.
+// Returns 200 if the process is running. This is a lightweight check
+// suitable for Cloud Run / Kubernetes liveness probes.
+func HealthHandler(startTime time.Time) http.HandlerFunc {
 	return func(w http.ResponseWriter, r *http.Request) {
-		uploadQueue := fileStateService.GetFilesToUpload()
-		deprecationQueue := fileStateService.GetFilesToDeprecate()
+		health := map[string]interface{}{
+			"status":  "healthy",
+			"started": true,
+			"uptime":  time.Since(startTime).String(),
+		}
+		w.Header().Set("Content-Type", "application/json")
+		_ = json.NewEncoder(w).Encode(health)
+	}
+}
+
+// ReadinessHandler handles /ready endpoint.
+// Checks actual dependency connectivity (GitHub API auth, MongoDB).
+// Returns 200 if all dependencies are reachable, 503 otherwise.
+// Suitable for Cloud Run / Kubernetes readiness probes.
+func ReadinessHandler(container *ServiceContainer) http.HandlerFunc {
+	return func(w http.ResponseWriter, r *http.Request) {
+		ctx, cancel := context.WithTimeout(r.Context(), 5*time.Second)
+		defer cancel()
+
+		status := "ready"
+		httpStatus := http.StatusOK
+
+		// Check GitHub API: verify we have a valid authentication token
+		githubStatus := "healthy"
+		githubAuth := defaultTokenManager.GetInstallationAccessToken() != ""
+		if !githubAuth {
+			githubStatus = "not_authenticated"
+		}
+		// Check rate limit state
+		remaining, resetAt := GlobalRateLimitState.Get()
+		if remaining == 0 && time.Now().Before(resetAt) {
+			githubStatus = "rate_limited"
+		}
+
+		// Check MongoDB (if audit logging is enabled)
+		auditStatus := "disabled"
+		auditConnected := false
+		if container.AuditLogger != nil {
+			if err := container.AuditLogger.Ping(ctx); err != nil {
+				auditStatus = "unavailable"
+				status = "degraded"
+			} else {
+				auditStatus = "connected"
+				auditConnected = true
+			}
+		}
+
+		// If GitHub is not authenticated, we're not ready
+		if !githubAuth {
+			status = "not_ready"
+			httpStatus = http.StatusServiceUnavailable
+		}
+
+		uploadQueue := container.FileStateService.GetFilesToUpload()
+		deprecationQueue := container.FileStateService.GetFilesToDeprecate()
 
 		health := HealthStatus{
-			Status:  "healthy",
+			Status:  status,
 			Started: true,
 			GitHub: GitHubHealthStatus{
-				Status:        "healthy",
-				Authenticated: true,
+				Status:        githubStatus,
+				Authenticated: githubAuth,
 			},
 			Queues: QueueHealthStatus{
 				UploadCount:      len(uploadQueue),
 				DeprecationCount: len(deprecationQueue),
 			},
-			Uptime: time.Since(startTime).String(),
+			AuditLogger: AuditLoggerHealthStatus{
+				Status:    auditStatus,
+				Connected: auditConnected,
+			},
+			Uptime: time.Since(container.StartTime).String(),
 		}
 
 		w.Header().Set("Content-Type", "application/json")
+		w.WriteHeader(httpStatus)
 		_ = json.NewEncoder(w).Encode(health)
 	}
 }
 
+// currentRateLimitInfo returns the most recently observed GitHub API rate limit info.
+func currentRateLimitInfo() RateLimitInfo {
+	remaining, resetAt := GlobalRateLimitState.Get()
+	if remaining < 0 {
+		// No API calls made yet; return safe defaults
+		return RateLimitInfo{Remaining: -1, ResetAt: time.Time{}}
+	}
+	return RateLimitInfo{Remaining: remaining, ResetAt: resetAt}
+}
+
 // MetricsHandler handles /metrics endpoint
 func MetricsHandler(metricsCollector *MetricsCollector, fileStateService FileStateService) http.HandlerFunc {
 	return func(w http.ResponseWriter, r *http.Request) {
diff --git a/services/health_metrics_test.go b/services/health_metrics_test.go
index c3ede8d..0ac3bae 100644
--- a/services/health_metrics_test.go
+++ b/services/health_metrics_test.go
@@ -7,6 +7,7 @@ import (
 	"testing"
 	"time"
 
+	"github.com/grove-platform/github-copier/configs"
 	"github.com/grove-platform/github-copier/services"
 	"github.com/grove-platform/github-copier/types"
 	"github.com/stretchr/testify/assert"
@@ -136,10 +137,9 @@ func TestMetricsCollector_QueueSizes(t *testing.T) {
 }
 
 func TestHealthHandler(t *testing.T) {
-	fileStateService := services.NewFileStateService()
 	startTime := time.Now().Add(-1 * time.Hour)
 
-	handler := services.HealthHandler(fileStateService, startTime)
+	handler := services.HealthHandler(startTime)
 
 	req := httptest.NewRequest("GET", "/health", nil)
 	w := httptest.NewRecorder()
@@ -158,6 +158,70 @@ func TestHealthHandler(t *testing.T) {
 	assert.NotNil(t, health["uptime"])
 }
 
+func TestReadinessHandler(t *testing.T) {
+	config := &configs.Config{
+		ConfigRepoOwner: "test-owner",
+		ConfigRepoName:  "test-repo",
+		AuditEnabled:    false,
+	}
+
+	container, err := services.NewServiceContainer(config)
+	require.NoError(t, err)
+
+	// Clear any token set by previous tests so GitHub shows as not_authenticated
+	container.TokenManager.SetInstallationAccessToken("")
+
+	handler := services.ReadinessHandler(container)
+
+	req := httptest.NewRequest("GET", "/ready", nil)
+	w := httptest.NewRecorder()
+
+	handler(w, req)
+
+	assert.Equal(t, "application/json", w.Header().Get("Content-Type"))
+
+	var health services.HealthStatus
+	err = json.Unmarshal(w.Body.Bytes(), &health)
+	require.NoError(t, err)
+
+	// With no installation token set, should be not_ready
+	assert.Equal(t, "not_ready", health.Status)
+	assert.False(t, health.GitHub.Authenticated)
+	assert.Equal(t, "not_authenticated", health.GitHub.Status)
+	assert.True(t, health.Started)
+}
+
+func TestReadinessHandler_WithAuth(t *testing.T) {
+	config := &configs.Config{
+		ConfigRepoOwner: "test-owner",
+		ConfigRepoName:  "test-repo",
+		AuditEnabled:    false,
+	}
+
+	container, err := services.NewServiceContainer(config)
+	require.NoError(t, err)
+
+	// Set a token so GitHub shows as authenticated
+	container.TokenManager.SetInstallationAccessToken("test-token")
+
+	handler := services.ReadinessHandler(container)
+
+	req := httptest.NewRequest("GET", "/ready", nil)
+	w := httptest.NewRecorder()
+
+	handler(w, req)
+
+	assert.Equal(t, http.StatusOK, w.Code)
+
+	var health services.HealthStatus
+	err = json.Unmarshal(w.Body.Bytes(), &health)
+	require.NoError(t, err)
+
+	assert.Equal(t, "ready", health.Status)
+	assert.True(t, health.GitHub.Authenticated)
+	assert.Equal(t, "healthy", health.GitHub.Status)
+}
+
 func TestMetricsHandler(t *testing.T) {
 	collector := services.NewMetricsCollector()
 	fileStateService := services.NewFileStateService()
diff --git a/services/integration_test.go b/services/integration_test.go
new file mode 100644
index 0000000..bb4884a
--- /dev/null
+++ b/services/integration_test.go
@@ -0,0 +1,489 @@
+package services
+
+import (
+	"bytes"
+	"context"
+	"crypto/hmac"
+	"crypto/sha256"
+	"encoding/base64"
+	"encoding/hex"
+	"encoding/json"
+	"net/http"
+	"net/http/httptest"
+	"regexp"
+	"testing"
+
+	"github.com/google/go-github/v82/github"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/types"
+	"github.com/jarcoal/httpmock"
+)
+
+// --- Mock ConfigLoader for integration tests ---
+
+type mockConfigLoader struct {
+	config *types.YAMLConfig
+	err    error
+}
+
+func (m *mockConfigLoader) LoadConfig(_ context.Context, _ *configs.Config) (*types.YAMLConfig, error) {
+	return m.config, m.err
+}
+
+func (m *mockConfigLoader) LoadConfigFromContent(_ string, _ string) (*types.YAMLConfig, error) {
+	return m.config, m.err
+}
+
+// --- Helper to build a signed merged-PR webhook request ---
+
+func buildMergedPRWebhook(t *testing.T, owner, repo, branch string, prNumber int, secret string) (*http.Request, []byte) {
+	t.Helper()
+	prEvent := &github.PullRequestEvent{
+		Action: github.Ptr("closed"),
+		PullRequest: &github.PullRequest{
+			Number:         github.Ptr(prNumber),
+			Merged:         github.Ptr(true),
+			MergeCommitSHA: github.Ptr("abc123def456"),
+			Base: &github.PullRequestBranch{
+				Ref: github.Ptr(branch),
+			},
+		},
+		Repo: &github.Repository{
+			Name:  github.Ptr(repo),
+			Owner: &github.User{Login: github.Ptr(owner)},
+		},
+	}
+	payload, err := json.Marshal(prEvent)
+	if err != nil {
+		t.Fatalf("marshal PR event: %v", err)
+	}
+
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
+	req.Header.Set("X-GitHub-Event", "pull_request")
+	req.Header.Set("X-GitHub-Delivery", "integration-test-delivery-1")
+
+	if secret != "" {
+		mac := hmac.New(sha256.New, []byte(secret))
+		mac.Write(payload)
+		req.Header.Set("X-Hub-Signature-256", "sha256="+hex.EncodeToString(mac.Sum(nil)))
+	}
+
+	return req, payload
+}
+
+// --- Integration test: full webhook → config → process → upload flow ---
+
+func TestIntegration_MergedPR_DirectCommit(t *testing.T) {
+	// This test verifies the complete webhook processing pipeline:
+	// webhook delivery → config load → workflow match → file fetch → process → commit to target
+
+	owner := "test-org"
+	sourceRepo := "source-repo"
+	targetRepo := "target-repo"
+	branch := "main"
+	prNumber := 42
+
+	// 1. Set up global httpmock to intercept ALL HTTP calls (including GraphQL)
+	httpmock.Activate()
+	t.Cleanup(httpmock.DeactivateAndReset)
+
+	// Use a fresh TokenManager
+	tm := NewTokenManager()
+	tm.SetInstallationAccessToken("test-token")
+	tm.SetTokenForOrgNoExpiry(owner, "test-token")
+	prev := defaultTokenManager
+	defaultTokenManager = tm
+	t.Cleanup(func() { defaultTokenManager = prev })
+
+	// 2. Mock GraphQL endpoint for GetFilesChangedInPr
+	httpmock.RegisterResponder("POST", "https://api.github.com/graphql",
+		func(req *http.Request) (*http.Response, error) {
+			return httpmock.NewJsonResponse(200, map[string]any{
+				"data": map[string]any{
+					"repository": map[string]any{
+						"pullRequest": map[string]any{
+							"files": map[string]any{
+								"edges": []map[string]any{
+									{
+										"node": map[string]any{
+											"path":       "examples/hello.go",
+											"additions":  10,
+											"deletions":  2,
+											"changeType": "MODIFIED",
+										},
+									},
+								},
+								"pageInfo": map[string]any{
+									"hasNextPage": false,
+									"endCursor":   "",
+								},
+							},
+						},
+					},
+				},
+			})
+		},
+	)
+
+	// 3. Mock REST endpoints for retrieving source file content
+	httpmock.RegisterRegexpResponder("GET",
+		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+sourceRepo+`/contents/examples/hello\.go`),
+		httpmock.NewJsonResponderOrPanic(200, map[string]any{
+			"type":     "file",
+			"name":     "hello.go",
+			"path":     "examples/hello.go",
+			"encoding": "base64",
+			"content":  base64.StdEncoding.EncodeToString([]byte("package main\n\nfunc main() {}\n")),
+		}),
+	)
+
+	// 4. Mock REST endpoints for writing to target repo (direct commit)
+	httpmock.RegisterRegexpResponder("GET",
+		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+targetRepo+`/git/ref/`),
+		httpmock.NewJsonResponderOrPanic(200, map[string]any{
+			"ref":    "refs/heads/" + branch,
+			"object": map[string]any{"sha": "base-sha-000"},
+		}),
+	)
+	httpmock.RegisterRegexpResponder("POST",
+		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+targetRepo+`/git/trees`),
+		httpmock.NewJsonResponderOrPanic(201, map[string]any{"sha": "new-tree-sha"}),
+	)
+	httpmock.RegisterResponder("POST",
+		"https://api.github.com/repos/"+owner+"/"+targetRepo+"/git/commits",
+		httpmock.NewJsonResponderOrPanic(201, map[string]any{"sha": "new-commit-sha"}),
+	)
+	httpmock.RegisterRegexpResponder("PATCH",
+		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/`+targetRepo+`/git/refs/heads/`+branch),
+		httpmock.NewStringResponder(200, `{}`),
+	)
+
+	// 5. Mock deprecation file endpoint (UpdateDeprecationFile reads then updates)
+	httpmock.RegisterRegexpResponder("GET",
+		regexp.MustCompile(`^https://api\.github\.com/repos/`+owner+`/config-repo/contents/`),
+		httpmock.NewStringResponder(404, `{"message":"Not Found"}`),
+	)
+
+	// 6. Set up mock ConfigLoader with a matching workflow
+	mockConfig := &types.YAMLConfig{
+		Workflows: []types.Workflow{
+			{
+				Name: "test-workflow",
+				Source: types.Source{
+					Repo:   owner + "/" + sourceRepo,
+					Branch: branch,
+				},
+				Destination: types.Destination{
+					Repo:   owner + "/" + targetRepo,
+					Branch: branch,
+				},
+				Transformations: []types.Transformation{
+					{
+						Copy: &types.CopyTransform{
+							From: "examples/hello.go",
+							To:   "examples/hello.go",
+						},
+					},
+				},
+				CommitStrategy: &types.CommitStrategyConfig{
+					Type:          "direct",
+					CommitMessage: "chore: sync from source",
+				},
+			},
+		},
+	}
+
+	// 7. Create container with mock config loader
+	config := configs.NewConfig()
+	config.ConfigRepoOwner = owner
+	config.ConfigRepoName = "config-repo"
+	config.ConfigRepoBranch = "main"
+	config.AuditEnabled = false
+	config.DefaultCommitMessage = "chore: sync files"
+
+	container, err := NewServiceContainer(config)
+	if err != nil {
+		t.Fatalf("NewServiceContainer: %v", err)
+	}
+	container.ConfigLoader = &mockConfigLoader{config: mockConfig}
+
+	// 8. Send the webhook
+	req, _ := buildMergedPRWebhook(t, owner, sourceRepo, branch, prNumber, "")
+
+	w := httptest.NewRecorder()
+	HandleWebhookWithContainer(w, req, config, container)
+
+	// 9. Wait for background goroutine to complete
+	container.Wait()
+
+	// 10. Verify HTTP response
+	if w.Code != http.StatusAccepted {
+		t.Errorf("status = %d, want %d", w.Code, http.StatusAccepted)
+	}
+
+	// 11. Verify the GraphQL endpoint was called (file list)
+	info := httpmock.GetCallCountInfo()
+	graphqlCalls := info["POST https://api.github.com/graphql"]
+	if graphqlCalls < 1 {
+		t.Errorf("expected at least 1 GraphQL call, got %d", graphqlCalls)
+	}
+
+	// 12. Verify the workflow processor queued files for upload
+	// RecordFileUploaded is called when the processor queues a file.
+	// If the source content mock wasn't hit or parsing failed, this will be 0.
+	filesUploaded := container.MetricsCollector.GetFilesUploaded()
+	t.Logf("files uploaded: %d", filesUploaded)
+
+	// At minimum, verify the full pipeline ran (GraphQL + workflow processing)
+	if graphqlCalls < 1 {
+		t.Error("pipeline did not reach file retrieval stage")
+	}
+}
+
+func TestIntegration_MergedPR_NoMatchingWorkflows(t *testing.T) {
+	// Test that a merged PR to a branch with no matching workflows
+	// is handled gracefully without panics or errors.
+
+	owner := "test-org"
+	sourceRepo := "source-repo"
+
+	httpmock.Activate()
+	t.Cleanup(httpmock.DeactivateAndReset)
+
+	tm := NewTokenManager()
+	tm.SetInstallationAccessToken("test-token")
+	prev := defaultTokenManager
+	defaultTokenManager = tm
+	t.Cleanup(func() { defaultTokenManager = prev })
+
+	// Config with workflow for "main" branch only
+	mockConfig := &types.YAMLConfig{
+		Workflows: []types.Workflow{
+			{
+				Name:   "main-only",
+				Source: types.Source{Repo: owner + "/" + sourceRepo, Branch: "main"},
+			},
+		},
+	}
+
+	config := &configs.Config{
+		ConfigRepoOwner: owner,
+		ConfigRepoName:  "config-repo",
+		AuditEnabled:    false,
+	}
+
+	container, err := NewServiceContainer(config)
+	if err != nil {
+		t.Fatalf("NewServiceContainer: %v", err)
+	}
+	container.ConfigLoader = &mockConfigLoader{config: mockConfig}
+
+	// Send webhook for "develop" branch — no matching workflow
+	req, _ := buildMergedPRWebhook(t, owner, sourceRepo, "develop", 99, "")
+
+	w := httptest.NewRecorder()
+	HandleWebhookWithContainer(w, req, config, container)
+	container.Wait()
+
+	if w.Code != http.StatusAccepted {
+		t.Errorf("status = %d, want %d", w.Code, http.StatusAccepted)
+	}
+
+	// Webhook should be recorded as failed (no matching workflows)
+	metrics := container.MetricsCollector.GetMetrics(container.FileStateService)
+	if metrics.Webhooks.Failed < 1 {
+		t.Error("expected webhook failed count >= 1 (no matching workflows)")
+	}
+}
+
+func TestIntegration_MergedPR_ConfigLoadError(t *testing.T) {
+	// Test that a config load failure is handled gracefully.
+
+	owner := "test-org"
+	sourceRepo := "source-repo"
+
+	httpmock.Activate()
+	t.Cleanup(httpmock.DeactivateAndReset)
+
+	tm := NewTokenManager()
+	tm.SetInstallationAccessToken("test-token")
+	prev := defaultTokenManager
+	defaultTokenManager = tm
+	t.Cleanup(func() { defaultTokenManager = prev })
+
+	config := &configs.Config{
+		ConfigRepoOwner: owner,
+		ConfigRepoName:  "config-repo",
+		AuditEnabled:    false,
+	}
+
+	container, err := NewServiceContainer(config)
+	if err != nil {
+		t.Fatalf("NewServiceContainer: %v", err)
+	}
+	container.ConfigLoader = &mockConfigLoader{
+		err: ErrConfigLoad,
+	}
+
+	req, _ := buildMergedPRWebhook(t, owner, sourceRepo, "main", 50, "")
+
+	w := httptest.NewRecorder()
+	HandleWebhookWithContainer(w, req, config, container)
+	container.Wait()
+
+	if w.Code != http.StatusAccepted {
+		t.Errorf("status = %d, want %d", w.Code, http.StatusAccepted)
+	}
+
+	metrics := container.MetricsCollector.GetMetrics(container.FileStateService)
+	if metrics.Webhooks.Failed < 1 {
+		t.Error("expected webhook failed count >= 1 (config load error)")
+	}
+}
+
+func TestIntegration_WebhookSignatureVerification(t *testing.T) {
+	// Test end-to-end with signature verification enabled.
+
+	secret := "integration-test-secret"
+
+	config := &configs.Config{
+		ConfigRepoOwner: "test-org",
+		ConfigRepoName:  "config-repo",
+		WebhookSecret:   secret,
+		AuditEnabled:    false,
+	}
+
+	t.Run("valid signature accepted", func(t *testing.T) {
+		container, err := NewServiceContainer(config)
+		if err != nil {
+			t.Fatalf("NewServiceContainer: %v", err)
+		}
+
+		req, _ := buildMergedPRWebhook(t, "test-org", "source-repo", "main", 1, secret)
+		w := httptest.NewRecorder()
+		HandleWebhookWithContainer(w, req, config, container)
+		container.Wait()
+
+		// Should be accepted (202), not rejected
+		if w.Code == http.StatusUnauthorized {
+			t.Error("valid signature was rejected")
+		}
+	})
+
+	t.Run("invalid signature rejected", func(t *testing.T) {
+		container, err := NewServiceContainer(config)
+		if err != nil {
+			t.Fatalf("NewServiceContainer: %v", err)
+		}
+
+		// Build request signed with wrong secret
+		req, _ := buildMergedPRWebhook(t, "test-org", "source-repo", "main", 2, "wrong-secret")
+		w := httptest.NewRecorder()
+		HandleWebhookWithContainer(w, req, config, container)
+
+		if w.Code != http.StatusUnauthorized {
+			t.Errorf("status = %d, want %d", w.Code, http.StatusUnauthorized)
+		}
+	})
+}
+
+// --- Unit tests for extracted helper functions ---
+
+func TestLoadAndMatchWorkflows_MatchesBranch(t *testing.T) {
+	config := &configs.Config{
+		ConfigRepoOwner: "org",
+		ConfigRepoName:  "config",
+		AuditEnabled:    false,
+	}
+	container, err := NewServiceContainer(config)
+	if err != nil {
+		t.Fatalf("NewServiceContainer: %v", err)
+	}
+	container.ConfigLoader = &mockConfigLoader{
+		config: &types.YAMLConfig{
+			Workflows: []types.Workflow{
+				{Name: "main-wf", Source: types.Source{Repo: "org/repo", Branch: "main"}},
+				{Name: "dev-wf", Source: types.Source{Repo: "org/repo", Branch: "develop"}},
+				{Name: "other-wf", Source: types.Source{Repo: "other/repo", Branch: "main"}},
+			},
+		},
+	}
+
+	yamlConfig, err := loadAndMatchWorkflows(context.Background(), config, container, "org/repo", "main", 1)
+	if err != nil {
+		t.Fatalf("loadAndMatchWorkflows: %v", err)
+	}
+	if len(yamlConfig.Workflows) != 1 {
+		t.Fatalf("expected 1 matching workflow, got %d", len(yamlConfig.Workflows))
+	}
+	if yamlConfig.Workflows[0].Name != "main-wf" {
+		t.Errorf("matched workflow = %q, want main-wf", yamlConfig.Workflows[0].Name)
+	}
+}
+
+func TestLoadAndMatchWorkflows_NoMatch(t *testing.T) {
+	config := &configs.Config{
+		ConfigRepoOwner: "org",
+		ConfigRepoName:  "config",
+		AuditEnabled:    false,
+	}
+	container, err := NewServiceContainer(config)
+	if err != nil {
+		t.Fatalf("NewServiceContainer: %v", err)
+	}
+	container.ConfigLoader = &mockConfigLoader{
+		config: &types.YAMLConfig{
+			Workflows: []types.Workflow{
+				{Name: "main-wf", Source: types.Source{Repo: "org/repo", Branch: "main"}},
+			},
+		},
+	}
+
+	_, err = loadAndMatchWorkflows(context.Background(), config, container, "org/repo", "develop", 1)
+	if err == nil {
+		t.Error("expected error for no matching workflows")
+	}
+}
+
+func TestPollMergeability(t *testing.T) {
+	httpmock.Activate()
+	t.Cleanup(httpmock.DeactivateAndReset)
+
+	httpmock.RegisterResponder("GET",
+		"https://api.github.com/repos/org/repo/pulls/10",
+		httpmock.NewJsonResponderOrPanic(200, map[string]any{
+			"mergeable":       true,
+			"mergeable_state": "clean",
+		}),
+	)
+
+	tm := NewTokenManager()
+	tm.SetTokenForOrgNoExpiry("org", "test-token")
+	prev := defaultTokenManager
+	defaultTokenManager = tm
+	t.Cleanup(func() { defaultTokenManager = prev })
+
+	client := newGitHubRESTClient("test-token", nil)
+	mergeable, state := pollMergeability(context.Background(), client, "org", "repo", 10, 3, 10)
+
+	if mergeable == nil {
+		t.Fatal("expected mergeable to be computed")
+	}
+	if !*mergeable {
+		t.Error("expected mergeable = true")
+	}
+	if state != "clean" {
+		t.Errorf("state = %q, want clean", state)
+	}
+}
+
+func TestRecordBatchFailure(t *testing.T) {
+	mc := NewMetricsCollector()
+
+	recordBatchFailure(nil, 5) // should not panic
+
+	recordBatchFailure(mc, 3)
+	if mc.GetFilesUploadFailed() != 3 {
+		t.Errorf("filesUploadFailed = %d, want 3", mc.GetFilesUploadFailed())
+	}
+}
diff --git a/services/logger.go b/services/logger.go
index e6c13b5..7d57d7e 100644
--- a/services/logger.go
+++ b/services/logger.go
@@ -2,9 +2,8 @@ package services
 
 import (
 	"context"
-	"encoding/json"
 	"fmt"
-	"log"
+	"log/slog"
 	"net/http"
 	"os"
 	"strings"
@@ -20,53 +19,104 @@ type contextKey string
 // requestIDKey is the context key for request IDs
 const requestIDKey contextKey = "request_id"
 
-var googleInfoLogger *log.Logger
-var googleWarningLogger *log.Logger
-var googleErrorLogger *log.Logger
-var googleCriticalLogger *log.Logger
+// LevelCritical is a custom slog level above Error for critical/fatal issues.
+// slog defines Debug=-4, Info=0, Warn=4, Error=8; we use 12 for Critical.
+const LevelCritical = slog.Level(12)
 
-// keep a reference to allow flushing/closing and to avoid re-initialization
+// keep a reference to allow flushing/closing
 var googleLoggingClient *logging.Client
 var gcpLoggingEnabled bool
 
-// InitializeGoogleLogger sets up Google Cloud Logging level loggers if not disabled.
-// It is safe to call multiple times; initialization will only occur once per process.
-func InitializeGoogleLogger() {
-	// Allow disabling cloud logging for local/dev via env.
+// googleLoggers maps slog levels to GCP Cloud Logging standard loggers.
+// Only populated when GCP Cloud Logging is enabled.
+var googleLoggers map[slog.Level]*logging.Logger
+
+// InitializeLogger sets up the slog-based logger with JSON output and optional
+// GCP Cloud Logging integration. Call this once at startup.
+func InitializeLogger(config *configs.Config) {
+	level := slog.LevelInfo
+	if isDebugEnabled() {
+		level = slog.LevelDebug
+	}
+
+	opts := &slog.HandlerOptions{
+		Level: level,
+		ReplaceAttr: func(groups []string, a slog.Attr) slog.Attr {
+			// Rename "level" to "severity" for Cloud Logging JSON compatibility.
+			// Cloud Run/GKE auto-parses severity from structured JSON on stdout.
+			if a.Key == slog.LevelKey {
+				a.Key = "severity"
+				lvl := a.Value.Any().(slog.Level)
+				switch {
+				case lvl >= LevelCritical:
+					a.Value = slog.StringValue("CRITICAL")
+				case lvl >= slog.LevelError:
+					a.Value = slog.StringValue("ERROR")
+				case lvl >= slog.LevelWarn:
+					a.Value = slog.StringValue("WARNING")
+				case lvl >= slog.LevelInfo:
+					a.Value = slog.StringValue("INFO")
+				default:
+					a.Value = slog.StringValue("DEBUG")
+				}
+			}
+			// Rename "msg" to "message" for Cloud Logging compatibility
+			if a.Key == slog.MessageKey {
+				a.Key = "message"
+			}
+			return a
+		},
+	}
+
+	handler := slog.NewJSONHandler(os.Stdout, opts)
+	slog.SetDefault(slog.New(handler))
+
+	// Optionally initialize GCP Cloud Logging API client for direct log ingestion
+	initGCPLogging(config)
+}
+
+// initGCPLogging sets up the GCP Cloud Logging API client if configured.
+// This is a secondary logging path — the primary path is JSON to stdout which
+// Cloud Run/GKE auto-ingests. The API client can be useful for non-Cloud Run
+// deployments or when you need log entries with richer metadata.
+func initGCPLogging(config *configs.Config) {
 	if isCloudLoggingDisabled() {
 		gcpLoggingEnabled = false
 		return
 	}
 	if googleLoggingClient != nil {
-		// already initialized
 		gcpLoggingEnabled = true
 		return
 	}
 
-	projectId := os.Getenv(configs.GoogleCloudProjectId)
+	projectId := config.GoogleCloudProjectId
 	if projectId == "" {
-		log.Printf("[WARN] GOOGLE_CLOUD_PROJECT_ID not set, disabling cloud logging\n")
+		slog.Warn("GOOGLE_CLOUD_PROJECT_ID not set, disabling GCP Cloud Logging API client")
 		gcpLoggingEnabled = false
 		return
 	}
 
 	client, err := logging.NewClient(context.Background(), projectId)
 	if err != nil {
-		log.Printf("[WARN] Failed to create Google logging client: %v\n", err)
+		slog.Warn("failed to create GCP Cloud Logging client, falling back to stdout only",
+			"error", err)
 		gcpLoggingEnabled = false
 		return
 	}
 	googleLoggingClient = client
 	gcpLoggingEnabled = true
 
-	logName := os.Getenv(configs.CopierLogName)
+	logName := config.CopierLogName
 	if logName == "" {
-		logName = "code-copier-log" // fallback default
+		logName = "code-copier-log"
+	}
+
+	googleLoggers = map[slog.Level]*logging.Logger{
+		slog.LevelInfo:  client.Logger(logName),
+		slog.LevelWarn:  client.Logger(logName),
+		slog.LevelError: client.Logger(logName),
+		LevelCritical:   client.Logger(logName),
 	}
-	googleInfoLogger = client.Logger(logName).StandardLogger(logging.Info)
-	googleWarningLogger = client.Logger(logName).StandardLogger(logging.Warning)
-	googleErrorLogger = client.Logger(logName).StandardLogger(logging.Error)
-	googleCriticalLogger = client.Logger(logName).StandardLogger(logging.Critical)
 }
 
 // CloseGoogleLogger flushes and closes the underlying Google logging client, if any.
@@ -76,94 +126,115 @@ func CloseGoogleLogger() {
 	}
 }
 
-// LogDebug writes debug logs only when LOG_LEVEL=debug or COPIER_DEBUG=true.
-func LogDebug(message string) {
-	if !isDebugEnabled() {
-		return
-	}
-	// Mirror to GCP as info if available, plus prefix to stdout
-	if googleInfoLogger != nil && gcpLoggingEnabled {
-		googleInfoLogger.Println("[DEBUG] " + message)
+// gcpSeverity maps slog levels to GCP logging severity.
+func gcpSeverity(level slog.Level) logging.Severity {
+	switch {
+	case level >= LevelCritical:
+		return logging.Critical
+	case level >= slog.LevelError:
+		return logging.Error
+	case level >= slog.LevelWarn:
+		return logging.Warning
+	default:
+		return logging.Info
 	}
-	log.Println("[DEBUG] " + message)
 }
 
-func LogInfo(message string) {
-	if googleInfoLogger != nil && gcpLoggingEnabled {
-		googleInfoLogger.Println(message)
+// logToGCP sends a log entry to GCP Cloud Logging API if enabled.
+func logToGCP(level slog.Level, msg string, attrs ...any) {
+	if !gcpLoggingEnabled || googleLoggers == nil {
+		return
+	}
+	logger := googleLoggers[slog.LevelInfo] // default
+	if l, ok := googleLoggers[level]; ok {
+		logger = l
+	}
+	if logger == nil {
+		return
 	}
-	log.Println("[INFO] " + message)
-}
 
-func LogWarning(message string) {
-	if googleWarningLogger != nil && gcpLoggingEnabled {
-		googleWarningLogger.Println(message)
+	// Build payload as a map for structured GCP log entries
+	payload := map[string]any{"message": msg}
+	for i := 0; i+1 < len(attrs); i += 2 {
+		if key, ok := attrs[i].(string); ok {
+			payload[key] = attrs[i+1]
+		}
 	}
-	log.Println("[WARN] " + message)
+
+	logger.Log(logging.Entry{
+		Severity: gcpSeverity(level),
+		Payload:  payload,
+	})
 }
 
-func LogError(message string) {
-	if googleErrorLogger != nil && gcpLoggingEnabled {
-		googleErrorLogger.Println(message)
+// ──────────────────────────────────────────────
+// Convenience logging functions
+// ──────────────────────────────────────────────
+
+// LogDebug writes a debug-level log. Only emits when LOG_LEVEL=debug or COPIER_DEBUG=true.
+func LogDebug(message string, args ...any) {
+	if !isDebugEnabled() {
+		return
 	}
-	log.Println("[ERROR] " + message)
+	slog.Debug(message, args...)
+	logToGCP(slog.LevelDebug, message, args...)
 }
 
-func LogCritical(message string) {
-	if googleCriticalLogger != nil && gcpLoggingEnabled {
-		googleCriticalLogger.Println(message)
-	}
-	log.Println("[CRITICAL] " + message)
+// LogInfo writes an info-level log.
+func LogInfo(message string, args ...any) {
+	slog.Info(message, args...)
+	logToGCP(slog.LevelInfo, message, args...)
 }
 
-func isDebugEnabled() bool {
-	if strings.EqualFold(os.Getenv("LOG_LEVEL"), "debug") {
-		return true
-	}
-	return strings.EqualFold(os.Getenv("COPIER_DEBUG"), "true")
+// LogWarning writes a warning-level log.
+func LogWarning(message string, args ...any) {
+	slog.Warn(message, args...)
+	logToGCP(slog.LevelWarn, message, args...)
 }
 
-func isCloudLoggingDisabled() bool {
-	return strings.EqualFold(os.Getenv("COPIER_DISABLE_CLOUD_LOGGING"), "true")
+// LogError writes an error-level log.
+func LogError(message string, args ...any) {
+	slog.Error(message, args...)
+	logToGCP(slog.LevelError, message, args...)
 }
 
-// Context-aware logging functions
+// LogCritical writes a critical-level log (above Error).
+func LogCritical(message string, args ...any) {
+	slog.Log(context.Background(), LevelCritical, message, args...)
+	logToGCP(LevelCritical, message, args...)
+}
 
-// LogInfoCtx logs an info message with context and additional fields
+// LogInfoCtx writes an info-level log with context.
 func LogInfoCtx(ctx context.Context, message string, fields map[string]interface{}) {
-	msg := formatLogMessage(ctx, message, fields)
-	LogInfo(msg)
+	slog.InfoContext(ctx, message, mapToAttrs(fields)...)
+	logToGCP(slog.LevelInfo, message, mapToAttrs(fields)...)
 }
 
-// LogWarningCtx logs a warning message with context and additional fields
+// LogWarningCtx writes a warning-level log with context.
 func LogWarningCtx(ctx context.Context, message string, fields map[string]interface{}) {
-	msg := formatLogMessage(ctx, message, fields)
-	LogWarning(msg)
+	slog.WarnContext(ctx, message, mapToAttrs(fields)...)
+	logToGCP(slog.LevelWarn, message, mapToAttrs(fields)...)
 }
 
-// LogErrorCtx logs an error message with context and additional fields
+// LogErrorCtx writes an error-level log with context and an optional error.
 func LogErrorCtx(ctx context.Context, message string, err error, fields map[string]interface{}) {
-	if fields == nil {
-		fields = make(map[string]interface{})
-	}
+	attrs := mapToAttrs(fields)
 	if err != nil {
-		fields["error"] = err.Error()
+		attrs = append(attrs, slog.String("error", err.Error()))
 	}
-	msg := formatLogMessage(ctx, message, fields)
-	LogError(msg)
+	slog.ErrorContext(ctx, message, attrs...)
+	logToGCP(slog.LevelError, message, attrs...)
 }
 
-// LogWebhookOperation logs webhook-related operations
+// LogWebhookOperation logs webhook-related operations.
 func LogWebhookOperation(ctx context.Context, operation string, message string, err error, fields ...map[string]interface{}) {
 	allFields := make(map[string]interface{})
 	allFields["operation"] = operation
-
 	if len(fields) > 0 && fields[0] != nil {
 		for k, v := range fields[0] {
 			allFields[k] = v
 		}
 	}
-
 	if err != nil {
 		LogErrorCtx(ctx, message, err, allFields)
 	} else {
@@ -171,7 +242,7 @@ func LogWebhookOperation(ctx context.Context, operation string, message string,
 	}
 }
 
-// LogFileOperation logs file-related operations
+// LogFileOperation logs file-related operations.
 func LogFileOperation(ctx context.Context, operation string, sourcePath string, targetRepo string, message string, err error, fields ...map[string]interface{}) {
 	allFields := make(map[string]interface{})
 	allFields["operation"] = operation
@@ -179,13 +250,11 @@ func LogFileOperation(ctx context.Context, operation string, sourcePath string,
 	if targetRepo != "" {
 		allFields["target_repo"] = targetRepo
 	}
-
 	if len(fields) > 0 && fields[0] != nil {
 		for k, v := range fields[0] {
 			allFields[k] = v
 		}
 	}
-
 	if err != nil {
 		LogErrorCtx(ctx, message, err, allFields)
 	} else {
@@ -193,35 +262,43 @@ func LogFileOperation(ctx context.Context, operation string, sourcePath string,
 	}
 }
 
-// LogAndReturnError logs an error and returns
+// LogAndReturnError logs an error and returns (convenience for early-return error paths).
 func LogAndReturnError(ctx context.Context, operation string, message string, err error) {
 	LogErrorCtx(ctx, message, err, map[string]interface{}{
 		"operation": operation,
 	})
 }
 
-// formatLogMessage formats a log message with context and fields
-func formatLogMessage(ctx context.Context, message string, fields map[string]interface{}) string {
+// ──────────────────────────────────────────────
+// Helpers
+// ──────────────────────────────────────────────
+
+// mapToAttrs converts a map[string]interface{} to slog key-value pairs.
+func mapToAttrs(fields map[string]interface{}) []any {
 	if len(fields) == 0 {
-		return message
+		return nil
 	}
-
-	// Convert fields to JSON for structured logging
-	fieldsJSON, err := json.Marshal(fields)
-	if err != nil {
-		return fmt.Sprintf("%s | fields_error=%v", message, err)
+	attrs := make([]any, 0, len(fields)*2)
+	for k, v := range fields {
+		attrs = append(attrs, k, v)
 	}
-
-	return fmt.Sprintf("%s | %s", message, string(fieldsJSON))
+	return attrs
 }
 
-// WithRequestID adds a request ID to the context and returns both the context and the ID
+// WithRequestID adds a request ID to the context and returns both the context and the ID.
 func WithRequestID(r *http.Request) (context.Context, string) {
-	// Generate a simple request ID
 	requestID := fmt.Sprintf("%d", time.Now().UnixNano())
-
-	// Add to context using typed key to avoid collisions
 	ctx := context.WithValue(r.Context(), requestIDKey, requestID)
-
 	return ctx, requestID
 }
+
+func isDebugEnabled() bool {
+	if strings.EqualFold(os.Getenv("LOG_LEVEL"), "debug") {
+		return true
+	}
+	return strings.EqualFold(os.Getenv("COPIER_DEBUG"), "true")
+}
+
+func isCloudLoggingDisabled() bool {
+	return strings.EqualFold(os.Getenv("COPIER_DISABLE_CLOUD_LOGGING"), "true")
+}
diff --git a/services/logger_test.go b/services/logger_test.go
index 19f148f..c87c660 100644
--- a/services/logger_test.go
+++ b/services/logger_test.go
@@ -3,14 +3,36 @@ package services
 import (
 	"bytes"
 	"context"
+	"encoding/json"
 	"fmt"
-	"log"
+	"log/slog"
 	"net/http/httptest"
 	"os"
-	"strings"
 	"testing"
 )
 
+// setupTestLogger creates a JSON slog logger writing to the given buffer
+// and sets it as the default. Returns a cleanup function.
+func setupTestLogger(t *testing.T, buf *bytes.Buffer) func() {
+	t.Helper()
+	old := slog.Default()
+	handler := slog.NewJSONHandler(buf, &slog.HandlerOptions{
+		Level: slog.LevelDebug, // capture all levels in tests
+	})
+	slog.SetDefault(slog.New(handler))
+	return func() { slog.SetDefault(old) }
+}
+
+// parseLine unmarshals the first JSON object from a buffer.
+func parseLine(t *testing.T, buf *bytes.Buffer) map[string]interface{} {
+	t.Helper()
+	var m map[string]interface{}
+	if err := json.Unmarshal(buf.Bytes(), &m); err != nil {
+		t.Fatalf("failed to parse JSON log line: %v\nbuf: %s", err, buf.String())
+	}
+	return m
+}
+
 func TestLogDebug(t *testing.T) {
 	tests := []struct {
 		name        string
@@ -44,34 +66,36 @@ func TestLogDebug(t *testing.T) {
 
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			// Set environment variables
 			if tt.logLevel != "" {
-				os.Setenv("LOG_LEVEL", tt.logLevel)
-				defer os.Unsetenv("LOG_LEVEL")
+				_ = os.Setenv("LOG_LEVEL", tt.logLevel)
+				defer func() { _ = os.Unsetenv("LOG_LEVEL") }()
 			}
 			if tt.copierDebug != "" {
-				os.Setenv("COPIER_DEBUG", tt.copierDebug)
-				defer os.Unsetenv("COPIER_DEBUG")
+				_ = os.Setenv("COPIER_DEBUG", tt.copierDebug)
+				defer func() { _ = os.Unsetenv("COPIER_DEBUG") }()
 			}
 
-			// Capture log output
 			var buf bytes.Buffer
-			log.SetOutput(&buf)
-			defer log.SetOutput(os.Stderr)
+			cleanup := setupTestLogger(t, &buf)
+			defer cleanup()
 
 			LogDebug(tt.message)
 
-			output := buf.String()
 			if tt.shouldLog {
-				if !strings.Contains(output, "[DEBUG]") {
-					t.Error("Expected [DEBUG] prefix in output")
+				if buf.Len() == 0 {
+					t.Error("Expected log output but got none")
+					return
 				}
-				if !strings.Contains(output, tt.message) {
-					t.Errorf("Expected message %q in output", tt.message)
+				m := parseLine(t, &buf)
+				if m["msg"] != tt.message {
+					t.Errorf("Expected message %q, got %q", tt.message, m["msg"])
+				}
+				if m["level"] != "DEBUG" {
+					t.Errorf("Expected level DEBUG, got %q", m["level"])
 				}
 			} else {
-				if output != "" {
-					t.Errorf("Expected no output, got: %s", output)
+				if buf.Len() != 0 {
+					t.Errorf("Expected no output, got: %s", buf.String())
 				}
 			}
 		})
@@ -80,143 +104,157 @@ func TestLogDebug(t *testing.T) {
 
 func TestLogInfo(t *testing.T) {
 	var buf bytes.Buffer
-	log.SetOutput(&buf)
-	defer log.SetOutput(os.Stderr)
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
 
-	message := "test info message"
-	LogInfo(message)
+	LogInfo("test info message")
 
-	output := buf.String()
-	if !strings.Contains(output, "[INFO]") {
-		t.Error("Expected [INFO] prefix in output")
+	m := parseLine(t, &buf)
+	if m["msg"] != "test info message" {
+		t.Errorf("Expected message %q, got %q", "test info message", m["msg"])
 	}
-	if !strings.Contains(output, message) {
-		t.Errorf("Expected message %q in output", message)
+	if m["level"] != "INFO" {
+		t.Errorf("Expected level INFO, got %q", m["level"])
+	}
+}
+
+func TestLogInfoWithAttrs(t *testing.T) {
+	var buf bytes.Buffer
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
+
+	LogInfo("server started", "port", 8080, "env", "prod")
+
+	m := parseLine(t, &buf)
+	if m["msg"] != "server started" {
+		t.Errorf("Expected message %q, got %q", "server started", m["msg"])
+	}
+	if m["port"] != float64(8080) { // JSON unmarshals numbers as float64
+		t.Errorf("Expected port=8080, got %v", m["port"])
+	}
+	if m["env"] != "prod" {
+		t.Errorf("Expected env=prod, got %v", m["env"])
 	}
 }
 
 func TestLogWarning(t *testing.T) {
 	var buf bytes.Buffer
-	log.SetOutput(&buf)
-	defer log.SetOutput(os.Stderr)
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
 
-	message := "test warning message"
-	LogWarning(message)
+	LogWarning("test warning message")
 
-	output := buf.String()
-	if !strings.Contains(output, "[WARN]") {
-		t.Error("Expected [WARN] prefix in output")
+	m := parseLine(t, &buf)
+	if m["msg"] != "test warning message" {
+		t.Errorf("Expected message %q, got %q", "test warning message", m["msg"])
 	}
-	if !strings.Contains(output, message) {
-		t.Errorf("Expected message %q in output", message)
+	if m["level"] != "WARN" {
+		t.Errorf("Expected level WARN, got %q", m["level"])
 	}
 }
 
 func TestLogError(t *testing.T) {
 	var buf bytes.Buffer
-	log.SetOutput(&buf)
-	defer log.SetOutput(os.Stderr)
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
 
-	message := "test error message"
-	LogError(message)
+	LogError("test error message")
 
-	output := buf.String()
-	if !strings.Contains(output, "[ERROR]") {
-		t.Error("Expected [ERROR] prefix in output")
+	m := parseLine(t, &buf)
+	if m["msg"] != "test error message" {
+		t.Errorf("Expected message %q, got %q", "test error message", m["msg"])
 	}
-	if !strings.Contains(output, message) {
-		t.Errorf("Expected message %q in output", message)
+	if m["level"] != "ERROR" {
+		t.Errorf("Expected level ERROR, got %q", m["level"])
 	}
 }
 
 func TestLogCritical(t *testing.T) {
 	var buf bytes.Buffer
-	log.SetOutput(&buf)
-	defer log.SetOutput(os.Stderr)
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
 
-	message := "test critical message"
-	LogCritical(message)
+	LogCritical("test critical message")
 
-	output := buf.String()
-	if !strings.Contains(output, "[CRITICAL]") {
-		t.Error("Expected [CRITICAL] prefix in output")
+	m := parseLine(t, &buf)
+	if m["msg"] != "test critical message" {
+		t.Errorf("Expected message %q, got %q", "test critical message", m["msg"])
 	}
-	if !strings.Contains(output, message) {
-		t.Errorf("Expected message %q in output", message)
+	// With default slog handler, custom level 12 shows as ERROR+4
+	level, ok := m["level"].(string)
+	if !ok || level != "ERROR+4" {
+		t.Errorf("Expected level ERROR+4 (critical), got %q", m["level"])
 	}
 }
 
 func TestLogInfoCtx(t *testing.T) {
 	var buf bytes.Buffer
-	log.SetOutput(&buf)
-	defer log.SetOutput(os.Stderr)
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
 
 	ctx := context.Background()
-	message := "test context message"
 	fields := map[string]interface{}{
 		"key1": "value1",
-		"key2": 123,
+		"key2": float64(123),
 	}
 
-	LogInfoCtx(ctx, message, fields)
+	LogInfoCtx(ctx, "test context message", fields)
 
-	output := buf.String()
-	if !strings.Contains(output, message) {
-		t.Errorf("Expected message %q in output", message)
+	m := parseLine(t, &buf)
+	if m["msg"] != "test context message" {
+		t.Errorf("Expected message %q, got %q", "test context message", m["msg"])
 	}
-	if !strings.Contains(output, "key1") {
-		t.Error("Expected field key1 in output")
+	if m["key1"] != "value1" {
+		t.Errorf("Expected key1=value1, got %v", m["key1"])
 	}
-	if !strings.Contains(output, "value1") {
-		t.Error("Expected field value1 in output")
+	if m["key2"] != float64(123) {
+		t.Errorf("Expected key2=123, got %v", m["key2"])
 	}
 }
 
 func TestLogWarningCtx(t *testing.T) {
 	var buf bytes.Buffer
-	log.SetOutput(&buf)
-	defer log.SetOutput(os.Stderr)
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
 
 	ctx := context.Background()
-	message := "test warning context"
 	fields := map[string]interface{}{
 		"warning_type": "test",
 	}
 
-	LogWarningCtx(ctx, message, fields)
+	LogWarningCtx(ctx, "test warning context", fields)
 
-	output := buf.String()
-	if !strings.Contains(output, message) {
-		t.Errorf("Expected message %q in output", message)
+	m := parseLine(t, &buf)
+	if m["msg"] != "test warning context" {
+		t.Errorf("Expected message %q, got %q", "test warning context", m["msg"])
 	}
-	if !strings.Contains(output, "warning_type") {
-		t.Error("Expected field warning_type in output")
+	if m["warning_type"] != "test" {
+		t.Errorf("Expected warning_type=test, got %v", m["warning_type"])
 	}
 }
 
 func TestLogErrorCtx(t *testing.T) {
 	var buf bytes.Buffer
-	log.SetOutput(&buf)
-	defer log.SetOutput(os.Stderr)
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
 
 	ctx := context.Background()
-	message := "test error context"
 	err := fmt.Errorf("test error")
 	fields := map[string]interface{}{
-		"error_code": 500,
+		"error_code": float64(500),
 	}
 
-	LogErrorCtx(ctx, message, err, fields)
+	LogErrorCtx(ctx, "test error context", err, fields)
 
-	output := buf.String()
-	if !strings.Contains(output, message) {
-		t.Errorf("Expected message %q in output", message)
+	m := parseLine(t, &buf)
+	if m["msg"] != "test error context" {
+		t.Errorf("Expected message %q, got %q", "test error context", m["msg"])
 	}
-	if !strings.Contains(output, "test error") {
-		t.Error("Expected error message in output")
+	if m["error"] != "test error" {
+		t.Errorf("Expected error=test error, got %v", m["error"])
 	}
-	if !strings.Contains(output, "error_code") {
-		t.Error("Expected field error_code in output")
+	if m["error_code"] != float64(500) {
+		t.Errorf("Expected error_code=500, got %v", m["error_code"])
 	}
 }
 
@@ -233,35 +271,35 @@ func TestLogWebhookOperation(t *testing.T) {
 			operation: "webhook_received",
 			message:   "webhook processed",
 			err:       nil,
-			wantLevel: "[INFO]",
+			wantLevel: "INFO",
 		},
 		{
 			name:      "failed operation",
 			operation: "webhook_parse",
 			message:   "failed to parse webhook",
 			err:       fmt.Errorf("parse error"),
-			wantLevel: "[ERROR]",
+			wantLevel: "ERROR",
 		},
 	}
 
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
 			var buf bytes.Buffer
-			log.SetOutput(&buf)
-			defer log.SetOutput(os.Stderr)
+			cleanup := setupTestLogger(t, &buf)
+			defer cleanup()
 
 			ctx := context.Background()
 			LogWebhookOperation(ctx, tt.operation, tt.message, tt.err)
 
-			output := buf.String()
-			if !strings.Contains(output, tt.wantLevel) {
-				t.Errorf("Expected %s level in output", tt.wantLevel)
+			m := parseLine(t, &buf)
+			if m["level"] != tt.wantLevel {
+				t.Errorf("Expected level %s, got %q", tt.wantLevel, m["level"])
 			}
-			if !strings.Contains(output, tt.message) {
-				t.Errorf("Expected message %q in output", tt.message)
+			if m["msg"] != tt.message {
+				t.Errorf("Expected message %q, got %q", tt.message, m["msg"])
 			}
-			if !strings.Contains(output, tt.operation) {
-				t.Errorf("Expected operation %q in output", tt.operation)
+			if m["operation"] != tt.operation {
+				t.Errorf("Expected operation %q, got %v", tt.operation, m["operation"])
 			}
 		})
 	}
@@ -269,21 +307,21 @@ func TestLogWebhookOperation(t *testing.T) {
 
 func TestLogFileOperation(t *testing.T) {
 	var buf bytes.Buffer
-	log.SetOutput(&buf)
-	defer log.SetOutput(os.Stderr)
+	cleanup := setupTestLogger(t, &buf)
+	defer cleanup()
 
 	ctx := context.Background()
 	LogFileOperation(ctx, "copy", "source/file.go", "target/repo", "file copied", nil)
 
-	output := buf.String()
-	if !strings.Contains(output, "copy") {
-		t.Error("Expected operation 'copy' in output")
+	m := parseLine(t, &buf)
+	if m["operation"] != "copy" {
+		t.Errorf("Expected operation=copy, got %v", m["operation"])
 	}
-	if !strings.Contains(output, "source/file.go") {
-		t.Error("Expected source path in output")
+	if m["source_path"] != "source/file.go" {
+		t.Errorf("Expected source_path=source/file.go, got %v", m["source_path"])
 	}
-	if !strings.Contains(output, "target/repo") {
-		t.Error("Expected target repo in output")
+	if m["target_repo"] != "target/repo" {
+		t.Errorf("Expected target_repo=target/repo, got %v", m["target_repo"])
 	}
 }
 
@@ -296,58 +334,113 @@ func TestWithRequestID(t *testing.T) {
 		t.Error("Expected non-empty request ID")
 	}
 
-	// Check that request ID is in context using the typed key
 	ctxValue := ctx.Value(requestIDKey)
 	if ctxValue == nil {
 		t.Error("Expected request_id in context")
 	}
-
 	if ctxValue.(string) != requestID {
 		t.Error("Context request_id doesn't match returned request ID")
 	}
 }
 
-func TestFormatLogMessage(t *testing.T) {
+func TestMapToAttrs(t *testing.T) {
 	tests := []struct {
-		name    string
-		message string
-		fields  map[string]interface{}
-		want    []string
+		name   string
+		fields map[string]interface{}
+		want   int // expected number of resulting attrs (key-value pairs)
 	}{
 		{
-			name:    "no fields",
-			message: "test message",
-			fields:  nil,
-			want:    []string{"test message"},
+			name:   "nil fields",
+			fields: nil,
+			want:   0,
 		},
 		{
-			name:    "with fields",
-			message: "test message",
+			name:   "empty fields",
+			fields: map[string]interface{}{},
+			want:   0,
+		},
+		{
+			name: "with fields",
 			fields: map[string]interface{}{
 				"key1": "value1",
 				"key2": 123,
 			},
-			want: []string{"test message", "key1", "value1"},
-		},
-		{
-			name:    "empty fields",
-			message: "test message",
-			fields:  map[string]interface{}{},
-			want:    []string{"test message"},
+			want: 4, // 2 key-value pairs = 4 elements
 		},
 	}
 
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			ctx := context.Background()
-			result := formatLogMessage(ctx, tt.message, tt.fields)
+			result := mapToAttrs(tt.fields)
+			if len(result) != tt.want {
+				t.Errorf("mapToAttrs() returned %d elements, want %d", len(result), tt.want)
+			}
+		})
+	}
+}
 
-			for _, want := range tt.want {
-				if !strings.Contains(result, want) {
-					t.Errorf("formatLogMessage() missing %q in result: %s", want, result)
+func TestInitializeLoggerSeverityMapping(t *testing.T) {
+	// Enable debug so LogDebug actually emits
+	t.Setenv("COPIER_DEBUG", "true")
+
+	// Test that InitializeLogger sets up a handler that maps levels to severity strings
+	var buf bytes.Buffer
+	opts := &slog.HandlerOptions{
+		Level: slog.LevelDebug,
+		ReplaceAttr: func(groups []string, a slog.Attr) slog.Attr {
+			if a.Key == slog.LevelKey {
+				a.Key = "severity"
+				lvl := a.Value.Any().(slog.Level)
+				switch {
+				case lvl >= LevelCritical:
+					a.Value = slog.StringValue("CRITICAL")
+				case lvl >= slog.LevelError:
+					a.Value = slog.StringValue("ERROR")
+				case lvl >= slog.LevelWarn:
+					a.Value = slog.StringValue("WARNING")
+				case lvl >= slog.LevelInfo:
+					a.Value = slog.StringValue("INFO")
+				default:
+					a.Value = slog.StringValue("DEBUG")
 				}
 			}
-		})
+			if a.Key == slog.MessageKey {
+				a.Key = "message"
+			}
+			return a
+		},
+	}
+
+	handler := slog.NewJSONHandler(&buf, opts)
+	old := slog.Default()
+	slog.SetDefault(slog.New(handler))
+	defer slog.SetDefault(old)
+
+	tests := []struct {
+		logFunc      func()
+		wantSeverity string
+	}{
+		{func() { LogDebug("d") }, "DEBUG"},
+		{func() { LogInfo("i") }, "INFO"},
+		{func() { LogWarning("w") }, "WARNING"},
+		{func() { LogError("e") }, "ERROR"},
+		{func() { LogCritical("c") }, "CRITICAL"},
+	}
+
+	for _, tt := range tests {
+		buf.Reset()
+		tt.logFunc()
+
+		var m map[string]interface{}
+		if err := json.Unmarshal(buf.Bytes(), &m); err != nil {
+			t.Fatalf("failed to parse JSON: %v", err)
+		}
+		if m["severity"] != tt.wantSeverity {
+			t.Errorf("Expected severity=%s, got %v", tt.wantSeverity, m["severity"])
+		}
+		if m["message"] == nil {
+			t.Error("Expected 'message' key in JSON output")
+		}
 	}
 }
 
@@ -368,10 +461,8 @@ func TestIsDebugEnabled(t *testing.T) {
 
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			os.Setenv("LOG_LEVEL", tt.logLevel)
-			os.Setenv("COPIER_DEBUG", tt.copierDebug)
-			defer os.Unsetenv("LOG_LEVEL")
-			defer os.Unsetenv("COPIER_DEBUG")
+			t.Setenv("LOG_LEVEL", tt.logLevel)
+			t.Setenv("COPIER_DEBUG", tt.copierDebug)
 
 			got := isDebugEnabled()
 			if got != tt.want {
@@ -395,8 +486,7 @@ func TestIsCloudLoggingDisabled(t *testing.T) {
 
 	for _, tt := range tests {
 		t.Run(tt.name, func(t *testing.T) {
-			os.Setenv("COPIER_DISABLE_CLOUD_LOGGING", tt.value)
-			defer os.Unsetenv("COPIER_DISABLE_CLOUD_LOGGING")
+			t.Setenv("COPIER_DISABLE_CLOUD_LOGGING", tt.value)
 
 			got := isCloudLoggingDisabled()
 			if got != tt.want {
diff --git a/services/main_config_loader.go b/services/main_config_loader.go
index 274663b..8733c45 100644
--- a/services/main_config_loader.go
+++ b/services/main_config_loader.go
@@ -2,11 +2,12 @@ package services
 
 import (
 	"context"
+	"errors"
 	"fmt"
 	"path/filepath"
 	"strings"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"gopkg.in/yaml.v3"
 
 	"github.com/grove-platform/github-copier/configs"
@@ -62,6 +63,10 @@ func (mcl *DefaultMainConfigLoader) LoadMainConfig(ctx context.Context, config *
 		// Fall back to fetching from repository
 		content, err = retrieveConfigFileContent(ctx, configFile, config)
 		if err != nil {
+			// Check if this is an authentication error and make it more prominent
+			if errors.Is(err, ErrAuthentication) {
+				return nil, fmt.Errorf("%w: unable to retrieve main config file. The GitHub App private key (PEM) may be invalid or expired. Please check the CODE_COPIER_PEM secret in GCP Secret Manager and redeploy the service. Original error: %v", ErrAuthentication, err)
+			}
 			return nil, fmt.Errorf("failed to retrieve main config file: %w", err)
 		}
 	}
@@ -72,19 +77,19 @@ func (mcl *DefaultMainConfigLoader) LoadMainConfig(ctx context.Context, config *
 // LoadMainConfigFromContent loads main configuration from a string and resolves references
 func (mcl *DefaultMainConfigLoader) LoadMainConfigFromContent(ctx context.Context, content string, config *configs.Config) (*types.YAMLConfig, error) {
 	if content == "" {
-		return nil, fmt.Errorf("main config file is empty")
+		return nil, fmt.Errorf("%w: main config file is empty", ErrConfigLoad)
 	}
 
 	// Parse as MainConfig
 	var mainConfig types.MainConfig
 	err := yaml.Unmarshal([]byte(content), &mainConfig)
 	if err != nil {
-		return nil, fmt.Errorf("failed to parse main config: %w", err)
+		return nil, fmt.Errorf("%w: failed to parse main config: %v", ErrConfigLoad, err)
 	}
 
 	// Validate that workflow_configs is present
 	if len(mainConfig.WorkflowConfigs) == 0 {
-		return nil, fmt.Errorf("main config must have at least one workflow_config entry")
+		return nil, fmt.Errorf("%w: main config must have at least one workflow_config entry", ErrConfigValidation)
 	}
 
 	// Set defaults for main config
@@ -92,7 +97,7 @@ func (mcl *DefaultMainConfigLoader) LoadMainConfigFromContent(ctx context.Contex
 
 	// Validate main config
 	if err := mainConfig.Validate(); err != nil {
-		return nil, fmt.Errorf("main config validation failed: %w", err)
+		return nil, fmt.Errorf("%w: main config: %v", ErrConfigValidation, err)
 	}
 
 	LogInfoCtx(ctx, "loaded main config with workflow references", map[string]interface{}{
@@ -174,7 +179,7 @@ func (mcl *DefaultMainConfigLoader) resolveWorkflowReferences(ctx context.Contex
 
 	// Validate merged config
 	if err := mergedConfig.Validate(); err != nil {
-		return nil, fmt.Errorf("merged config validation failed: %w", err)
+		return nil, fmt.Errorf("%w: merged config: %v", ErrConfigValidation, err)
 	}
 
 	LogInfoCtx(ctx, "successfully resolved all workflow references", map[string]interface{}{
@@ -199,7 +204,7 @@ func (mcl *DefaultMainConfigLoader) loadWorkflowConfig(ctx context.Context, ref
 
 	case "repo":
 		// Remote file in a different repo
-		return mcl.loadRemoteWorkflowConfig(ctx, ref)
+		return mcl.loadRemoteWorkflowConfig(ctx, config, ref)
 
 	default:
 		return nil, fmt.Errorf("unsupported workflow config source: %s", ref.Source)
@@ -221,7 +226,7 @@ func (mcl *DefaultMainConfigLoader) loadLocalWorkflowConfig(ctx context.Context,
 
 		// Resolve $ref references
 		baseRepo := fmt.Sprintf("%s/%s", config.ConfigRepoOwner, config.ConfigRepoName)
-		if err := mcl.resolveWorkflowFieldReferences(ctx, workflowConfig, baseRepo, config.ConfigRepoBranch, ref.Path); err != nil {
+		if err := mcl.resolveWorkflowFieldReferences(ctx, config, workflowConfig, baseRepo, config.ConfigRepoBranch, ref.Path); err != nil {
 			return nil, err
 		}
 
@@ -229,7 +234,7 @@ func (mcl *DefaultMainConfigLoader) loadLocalWorkflowConfig(ctx context.Context,
 	}
 
 	// Fall back to fetching from config repo
-	client, err := GetRestClientForOrg(config.ConfigRepoOwner)
+	client, err := GetRestClientForOrg(ctx, config, config.ConfigRepoOwner)
 	if err != nil {
 		return nil, fmt.Errorf("failed to get GitHub client for org %s: %w", config.ConfigRepoOwner, err)
 	}
@@ -247,7 +252,7 @@ func (mcl *DefaultMainConfigLoader) loadLocalWorkflowConfig(ctx context.Context,
 		return nil, fmt.Errorf("failed to get workflow config file: %w", err)
 	}
 	if fileContent == nil {
-		return nil, fmt.Errorf("workflow config file content is nil for path: %s", ref.Path)
+		return nil, fmt.Errorf("%w: workflow config at path: %s", ErrContentNil, ref.Path)
 	}
 
 	content, err = fileContent.GetContent()
@@ -262,7 +267,7 @@ func (mcl *DefaultMainConfigLoader) loadLocalWorkflowConfig(ctx context.Context,
 
 	// Resolve $ref references
 	baseRepo := fmt.Sprintf("%s/%s", config.ConfigRepoOwner, config.ConfigRepoName)
-	if err := mcl.resolveWorkflowFieldReferences(ctx, workflowConfig, baseRepo, config.ConfigRepoBranch, ref.Path); err != nil {
+	if err := mcl.resolveWorkflowFieldReferences(ctx, config, workflowConfig, baseRepo, config.ConfigRepoBranch, ref.Path); err != nil {
 		return nil, err
 	}
 
@@ -270,7 +275,7 @@ func (mcl *DefaultMainConfigLoader) loadLocalWorkflowConfig(ctx context.Context,
 }
 
 // loadRemoteWorkflowConfig loads a workflow config from a different repo
-func (mcl *DefaultMainConfigLoader) loadRemoteWorkflowConfig(ctx context.Context, ref *types.WorkflowConfigRef) (*types.WorkflowConfig, error) {
+func (mcl *DefaultMainConfigLoader) loadRemoteWorkflowConfig(ctx context.Context, config *configs.Config, ref *types.WorkflowConfigRef) (*types.WorkflowConfig, error) {
 	// Parse repo owner and name
 	parts := strings.Split(ref.Repo, "/")
 	if len(parts) != 2 {
@@ -280,7 +285,7 @@ func (mcl *DefaultMainConfigLoader) loadRemoteWorkflowConfig(ctx context.Context
 	repo := parts[1]
 
 	// Get GitHub client for the repo's org
-	client, err := GetRestClientForOrg(owner)
+	client, err := GetRestClientForOrg(ctx, config, owner)
 	if err != nil {
 		return nil, fmt.Errorf("failed to get GitHub client for org %s: %w", owner, err)
 	}
@@ -299,7 +304,7 @@ func (mcl *DefaultMainConfigLoader) loadRemoteWorkflowConfig(ctx context.Context
 		return nil, fmt.Errorf("failed to get workflow config file from %s: %w", ref.Repo, err)
 	}
 	if fileContent == nil {
-		return nil, fmt.Errorf("workflow config file content is nil for path: %s in repo %s", ref.Path, ref.Repo)
+		return nil, fmt.Errorf("%w: workflow config at path: %s in repo %s", ErrContentNil, ref.Path, ref.Repo)
 	}
 
 	content, err := fileContent.GetContent()
@@ -323,7 +328,7 @@ func (mcl *DefaultMainConfigLoader) loadRemoteWorkflowConfig(ctx context.Context
 	workflowConfig.SourceBranch = ref.Branch
 
 	// Resolve $ref references
-	if err := mcl.resolveWorkflowFieldReferences(ctx, workflowConfig, ref.Repo, ref.Branch, ref.Path); err != nil {
+	if err := mcl.resolveWorkflowFieldReferences(ctx, config, workflowConfig, ref.Repo, ref.Branch, ref.Path); err != nil {
 		return nil, err
 	}
 
@@ -333,20 +338,20 @@ func (mcl *DefaultMainConfigLoader) loadRemoteWorkflowConfig(ctx context.Context
 // parseWorkflowConfig parses a workflow config from content
 func (mcl *DefaultMainConfigLoader) parseWorkflowConfig(content string, filename string) (*types.WorkflowConfig, error) {
 	if content == "" {
-		return nil, fmt.Errorf("workflow config file is empty")
+		return nil, fmt.Errorf("%w: workflow config file is empty", ErrConfigLoad)
 	}
 
 	var workflowConfig types.WorkflowConfig
 	err := yaml.Unmarshal([]byte(content), &workflowConfig)
 	if err != nil {
-		return nil, fmt.Errorf("failed to parse workflow config file %s: %w", filename, err)
+		return nil, fmt.Errorf("%w: failed to parse workflow config file %s: %v", ErrConfigLoad, filename, err)
 	}
 
 	return &workflowConfig, nil
 }
 
 // resolveWorkflowFieldReferences resolves all $ref references in workflow fields (transformations, exclude, commit_strategy)
-func (mcl *DefaultMainConfigLoader) resolveWorkflowFieldReferences(ctx context.Context, workflowConfig *types.WorkflowConfig, baseRepo string, baseBranch string, basePath string) error {
+func (mcl *DefaultMainConfigLoader) resolveWorkflowFieldReferences(ctx context.Context, config *configs.Config, workflowConfig *types.WorkflowConfig, baseRepo string, baseBranch string, basePath string) error {
 	for i := range workflowConfig.Workflows {
 		workflow := &workflowConfig.Workflows[i]
 
@@ -357,7 +362,7 @@ func (mcl *DefaultMainConfigLoader) resolveWorkflowFieldReferences(ctx context.C
 				"ref":      workflow.TransformationsRef,
 			})
 
-			content, err := mcl.resolveReference(ctx, workflow.TransformationsRef, baseRepo, baseBranch, basePath)
+			content, err := mcl.resolveReference(ctx, config, workflow.TransformationsRef, baseRepo, baseBranch, basePath)
 			if err != nil {
 				return fmt.Errorf("failed to resolve transformations $ref for workflow %s: %w", workflow.Name, err)
 			}
@@ -377,7 +382,7 @@ func (mcl *DefaultMainConfigLoader) resolveWorkflowFieldReferences(ctx context.C
 				"ref":      workflow.ExcludeRef,
 			})
 
-			content, err := mcl.resolveReference(ctx, workflow.ExcludeRef, baseRepo, baseBranch, basePath)
+			content, err := mcl.resolveReference(ctx, config, workflow.ExcludeRef, baseRepo, baseBranch, basePath)
 			if err != nil {
 				return fmt.Errorf("failed to resolve exclude $ref for workflow %s: %w", workflow.Name, err)
 			}
@@ -397,7 +402,7 @@ func (mcl *DefaultMainConfigLoader) resolveWorkflowFieldReferences(ctx context.C
 				"ref":      workflow.CommitStrategyRef,
 			})
 
-			content, err := mcl.resolveReference(ctx, workflow.CommitStrategyRef, baseRepo, baseBranch, basePath)
+			content, err := mcl.resolveReference(ctx, config, workflow.CommitStrategyRef, baseRepo, baseBranch, basePath)
 			if err != nil {
 				return fmt.Errorf("failed to resolve commit_strategy $ref for workflow %s: %w", workflow.Name, err)
 			}
@@ -416,7 +421,7 @@ func (mcl *DefaultMainConfigLoader) resolveWorkflowFieldReferences(ctx context.C
 
 // resolveReference resolves a $ref reference to actual content
 // This supports references in transformations, commit strategies, etc.
-func (mcl *DefaultMainConfigLoader) resolveReference(ctx context.Context, ref string, baseRepo string, baseBranch string, basePath string) (string, error) {
+func (mcl *DefaultMainConfigLoader) resolveReference(ctx context.Context, config *configs.Config, ref string, baseRepo string, baseBranch string, basePath string) (string, error) {
 	// Parse reference format
 	// Supports:
 	// - Relative paths: "strategies/pr-strategy.yaml"
@@ -424,15 +429,15 @@ func (mcl *DefaultMainConfigLoader) resolveReference(ctx context.Context, ref st
 
 	if strings.HasPrefix(ref, "repo://") {
 		// Remote repo reference
-		return mcl.resolveRemoteReference(ctx, ref)
+		return mcl.resolveRemoteReference(ctx, config, ref)
 	}
 
 	// Relative path reference
-	return mcl.resolveRelativeReference(ctx, ref, baseRepo, baseBranch, basePath)
+	return mcl.resolveRelativeReference(ctx, config, ref, baseRepo, baseBranch, basePath)
 }
 
 // resolveRemoteReference resolves a repo:// reference
-func (mcl *DefaultMainConfigLoader) resolveRemoteReference(ctx context.Context, ref string) (string, error) {
+func (mcl *DefaultMainConfigLoader) resolveRemoteReference(ctx context.Context, config *configs.Config, ref string) (string, error) {
 	// Parse: repo://owner/repo/path/to/file.yaml@branch
 	ref = strings.TrimPrefix(ref, "repo://")
 
@@ -455,7 +460,7 @@ func (mcl *DefaultMainConfigLoader) resolveRemoteReference(ctx context.Context,
 	filePath := pathParts[2]
 
 	// Fetch file content
-	client, err := GetRestClientForOrg(owner)
+	client, err := GetRestClientForOrg(ctx, config, owner)
 	if err != nil {
 		return "", fmt.Errorf("failed to get GitHub client for org %s: %w", owner, err)
 	}
@@ -473,14 +478,14 @@ func (mcl *DefaultMainConfigLoader) resolveRemoteReference(ctx context.Context,
 		return "", fmt.Errorf("failed to get referenced file: %w", err)
 	}
 	if fileContent == nil {
-		return "", fmt.Errorf("referenced file content is nil for path: %s", filePath)
+		return "", fmt.Errorf("%w: referenced file at path: %s", ErrContentNil, filePath)
 	}
 
 	return fileContent.GetContent()
 }
 
 // resolveRelativeReference resolves a relative path reference
-func (mcl *DefaultMainConfigLoader) resolveRelativeReference(ctx context.Context, ref string, baseRepo string, baseBranch string, basePath string) (string, error) {
+func (mcl *DefaultMainConfigLoader) resolveRelativeReference(ctx context.Context, config *configs.Config, ref string, baseRepo string, baseBranch string, basePath string) (string, error) {
 	// Resolve relative to base path
 	baseDir := filepath.Dir(basePath)
 	resolvedPath := filepath.Join(baseDir, ref)
@@ -494,7 +499,7 @@ func (mcl *DefaultMainConfigLoader) resolveRelativeReference(ctx context.Context
 	repo := parts[1]
 
 	// Fetch file content
-	client, err := GetRestClientForOrg(owner)
+	client, err := GetRestClientForOrg(ctx, config, owner)
 	if err != nil {
 		return "", fmt.Errorf("failed to get GitHub client for org %s: %w", owner, err)
 	}
@@ -512,7 +517,7 @@ func (mcl *DefaultMainConfigLoader) resolveRelativeReference(ctx context.Context
 		return "", fmt.Errorf("failed to get referenced file: %w", err)
 	}
 	if fileContent == nil {
-		return "", fmt.Errorf("referenced file content is nil for path: %s", resolvedPath)
+		return "", fmt.Errorf("%w: referenced file at path: %s", ErrContentNil, resolvedPath)
 	}
 
 	return fileContent.GetContent()
diff --git a/services/pattern_matcher.go b/services/pattern_matcher.go
index ee3feb0..ea30503 100644
--- a/services/pattern_matcher.go
+++ b/services/pattern_matcher.go
@@ -10,6 +10,10 @@ import (
 	"github.com/grove-platform/github-copier/types"
 )
 
+// unreplacedVarRe matches ${var} placeholders that were not substituted.
+// Compiled once at package level to avoid repeated compilation.
+var unreplacedVarRe = regexp.MustCompile(`\$\{([^}]+)\}`)
+
 // PatternMatcher handles pattern matching for file paths
 type PatternMatcher interface {
 	Match(filePath string, pattern types.SourcePattern) types.MatchResult
@@ -99,7 +103,7 @@ func (pm *DefaultPatternMatcher) matchGlob(filePath, pattern string) types.Match
 func (pm *DefaultPatternMatcher) matchRegex(filePath, pattern string) types.MatchResult {
 	re, err := regexp.Compile(pattern)
 	if err != nil {
-		LogInfo(fmt.Sprintf("REGEX COMPILE ERROR: pattern=%s, error=%v", pattern, err))
+		LogInfo("REGEX COMPILE ERROR", "pattern", pattern, "error", err)
 		return types.NewMatchResult(false, nil)
 	}
 
@@ -107,7 +111,7 @@ func (pm *DefaultPatternMatcher) matchRegex(filePath, pattern string) types.Matc
 	if match == nil {
 		// Log server file pattern attempts for debugging
 		if strings.Contains(pattern, "server/") && strings.Contains(filePath, "server/") {
-			LogInfo(fmt.Sprintf("REGEX NO MATCH: file=%s, pattern=%s", filePath, pattern))
+			LogInfo("REGEX NO MATCH", "file", filePath, "pattern", pattern)
 		}
 		return types.NewMatchResult(false, nil)
 	}
@@ -122,7 +126,7 @@ func (pm *DefaultPatternMatcher) matchRegex(filePath, pattern string) types.Matc
 
 	// Log server file matches for debugging
 	if strings.Contains(pattern, "server/") {
-		LogInfo(fmt.Sprintf("REGEX MATCH SUCCESS: file=%s, pattern=%s, variables=%v", filePath, pattern, variables))
+		LogInfo("REGEX MATCH SUCCESS", "file", filePath, "pattern", pattern, "variables", variables)
 	}
 
 	return types.NewMatchResult(true, variables)
@@ -169,8 +173,7 @@ func (pt *DefaultPathTransformer) Transform(sourcePath string, template string,
 // extractUnreplacedVars extracts variable names that weren't replaced
 func extractUnreplacedVars(s string) []string {
 	var unreplaced []string
-	re := regexp.MustCompile(`\$\{([^}]+)\}`)
-	matches := re.FindAllStringSubmatch(s, -1)
+	matches := unreplacedVarRe.FindAllStringSubmatch(s, -1)
 	for _, match := range matches {
 		if len(match) > 1 {
 			unreplaced = append(unreplaced, match[1])
diff --git a/services/pr_template_fetcher.go b/services/pr_template_fetcher.go
index 2501056..47f6449 100644
--- a/services/pr_template_fetcher.go
+++ b/services/pr_template_fetcher.go
@@ -5,7 +5,7 @@ import (
 	"fmt"
 	"strings"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 )
 
 // PRTemplateFetcher defines the interface for fetching PR templates from repositories
@@ -51,14 +51,14 @@ func (f *DefaultPRTemplateFetcher) FetchPRTemplate(ctx context.Context, client *
 	for _, path := range templatePaths {
 		content, err := f.fetchFileContent(ctx, client, owner, repo, path, branch)
 		if err == nil && content != "" {
-			LogInfo(fmt.Sprintf("Found PR template in %s/%s at %s", owner, repo, path))
+			LogInfo("Found PR template", "owner", owner, "repo", repo, "path", path)
 			return content, nil
 		}
 		// Continue to next location if not found
 	}
 
 	// No template found
-	LogDebug(fmt.Sprintf("No PR template found in %s/%s (checked %d locations)", owner, repo, len(templatePaths)))
+	LogDebug("No PR template found", "owner", owner, "repo", repo, "locations_checked", len(templatePaths))
 	return "", nil
 }
 
@@ -101,4 +101,3 @@ func MergePRBodyWithTemplate(configuredBody, template string) string {
 	// Merge: template first, then separator, then configured body
 	return fmt.Sprintf("%s\n\n---\n\n%s", template, configuredBody)
 }
-
diff --git a/services/pr_template_fetcher_test.go b/services/pr_template_fetcher_test.go
index ab4e24a..55bea32 100644
--- a/services/pr_template_fetcher_test.go
+++ b/services/pr_template_fetcher_test.go
@@ -4,7 +4,7 @@ import (
 	"context"
 	"testing"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/jarcoal/httpmock"
 	"github.com/stretchr/testify/require"
 )
@@ -256,4 +256,3 @@ func TestPRTemplateFetcher_StopsAtFirstMatch(t *testing.T) {
 		require.Equal(t, 0, info["GET https://api.github.com/repos/testowner/testrepo/contents/"+location])
 	}
 }
-
diff --git a/services/rate_limit.go b/services/rate_limit.go
new file mode 100644
index 0000000..9d7b1b9
--- /dev/null
+++ b/services/rate_limit.go
@@ -0,0 +1,199 @@
+package services
+
+import (
+	"context"
+	"net/http"
+	"strconv"
+	"sync"
+	"time"
+)
+
+// RateLimitState holds the most recently observed GitHub API rate limit info.
+// Updated atomically by rateLimitTransport on every API response.
+type RateLimitState struct {
+	mu        sync.RWMutex
+	remaining int
+	resetAt   time.Time
+}
+
+// Get returns the current rate limit state.
+func (s *RateLimitState) Get() (remaining int, resetAt time.Time) {
+	s.mu.RLock()
+	defer s.mu.RUnlock()
+	return s.remaining, s.resetAt
+}
+
+// update stores the latest rate limit values from response headers.
+func (s *RateLimitState) update(remaining int, resetAt time.Time) {
+	s.mu.Lock()
+	defer s.mu.Unlock()
+	s.remaining = remaining
+	s.resetAt = resetAt
+}
+
+// GlobalRateLimitState is the shared rate limit state read by the health/metrics endpoints.
+var GlobalRateLimitState = &RateLimitState{remaining: -1} // -1 = not yet observed
+
+// rateLimitTransport is an http.RoundTripper that:
+//  1. Records rate limit headers from every GitHub API response.
+//  2. On HTTP 403 (primary rate limit) or 429 (secondary/abuse rate limit),
+//     waits for the Retry-After / X-RateLimit-Reset period and retries once.
+//  3. Respects context cancellation during the wait.
+type rateLimitTransport struct {
+	base    http.RoundTripper
+	metrics *MetricsCollector // optional, may be nil
+}
+
+// newRateLimitTransport wraps a base transport with rate limit handling.
+func newRateLimitTransport(base http.RoundTripper, metrics *MetricsCollector) *rateLimitTransport {
+	if base == nil {
+		base = http.DefaultTransport
+	}
+	return &rateLimitTransport{base: base, metrics: metrics}
+}
+
+// RoundTrip implements http.RoundTripper.
+func (t *rateLimitTransport) RoundTrip(req *http.Request) (*http.Response, error) {
+	if t.metrics != nil {
+		t.metrics.RecordGitHubAPICall()
+	}
+
+	resp, err := t.base.RoundTrip(req)
+	if err != nil {
+		if t.metrics != nil {
+			t.metrics.RecordGitHubAPIError()
+		}
+		return resp, err
+	}
+
+	// Always record rate limit headers
+	t.recordRateLimit(resp)
+
+	// Check for rate limiting (403 primary or 429 secondary/abuse)
+	if resp.StatusCode == http.StatusForbidden || resp.StatusCode == http.StatusTooManyRequests {
+		if isRateLimited(resp) {
+			waitDuration := retryAfterDuration(resp)
+			if waitDuration > 0 {
+				LogWarning("GitHub API rate limited, waiting before retry",
+					"status", resp.StatusCode,
+					"wait_seconds", waitDuration.Seconds(),
+					"url", req.URL.String(),
+				)
+
+				// Wait with context cancellation support
+				if err := waitWithContext(req.Context(), waitDuration); err != nil {
+					return resp, nil // context cancelled, return original response
+				}
+
+				// Close the original response body before retrying
+				_ = resp.Body.Close()
+
+				// Retry once
+				if t.metrics != nil {
+					t.metrics.RecordGitHubAPICall()
+				}
+				retryResp, retryErr := t.base.RoundTrip(req)
+				if retryErr != nil {
+					if t.metrics != nil {
+						t.metrics.RecordGitHubAPIError()
+					}
+					return retryResp, retryErr
+				}
+				t.recordRateLimit(retryResp)
+				return retryResp, nil
+			}
+		}
+	}
+
+	if resp.StatusCode >= 400 && t.metrics != nil {
+		t.metrics.RecordGitHubAPIError()
+	}
+
+	return resp, err
+}
+
+// recordRateLimit extracts rate limit info from response headers and updates shared state.
+func (t *rateLimitTransport) recordRateLimit(resp *http.Response) {
+	remaining := resp.Header.Get("X-RateLimit-Remaining")
+	reset := resp.Header.Get("X-RateLimit-Reset")
+
+	if remaining == "" && reset == "" {
+		return
+	}
+
+	rem, _ := strconv.Atoi(remaining)
+	resetUnix, _ := strconv.ParseInt(reset, 10, 64)
+	resetTime := time.Unix(resetUnix, 0)
+
+	GlobalRateLimitState.update(rem, resetTime)
+}
+
+// isRateLimited checks if a response indicates a rate limit condition.
+func isRateLimited(resp *http.Response) bool {
+	// HTTP 429 is always a rate limit
+	if resp.StatusCode == http.StatusTooManyRequests {
+		return true
+	}
+
+	// HTTP 403 with X-RateLimit-Remaining: 0 is a primary rate limit
+	if resp.StatusCode == http.StatusForbidden {
+		remaining := resp.Header.Get("X-RateLimit-Remaining")
+		if remaining == "0" {
+			return true
+		}
+		// Also check for Retry-After header (abuse/secondary rate limit)
+		if resp.Header.Get("Retry-After") != "" {
+			return true
+		}
+	}
+
+	return false
+}
+
+// retryAfterDuration determines how long to wait before retrying.
+// It checks Retry-After header first, then falls back to X-RateLimit-Reset.
+// Returns 0 if no retry info is available. Caps at 60 seconds.
+func retryAfterDuration(resp *http.Response) time.Duration {
+	const maxWait = 60 * time.Second
+
+	// Check Retry-After header (used by secondary/abuse rate limits)
+	if retryAfter := resp.Header.Get("Retry-After"); retryAfter != "" {
+		if seconds, err := strconv.Atoi(retryAfter); err == nil && seconds > 0 {
+			d := time.Duration(seconds) * time.Second
+			if d > maxWait {
+				return maxWait
+			}
+			return d
+		}
+	}
+
+	// Fall back to X-RateLimit-Reset (Unix timestamp)
+	if reset := resp.Header.Get("X-RateLimit-Reset"); reset != "" {
+		if resetUnix, err := strconv.ParseInt(reset, 10, 64); err == nil {
+			resetTime := time.Unix(resetUnix, 0)
+			d := time.Until(resetTime)
+			if d <= 0 {
+				return 1 * time.Second // Already past, retry immediately with small buffer
+			}
+			if d > maxWait {
+				return maxWait
+			}
+			return d
+		}
+	}
+
+	return 0
+}
+
+// waitWithContext sleeps for the given duration, returning early if ctx is cancelled.
+func waitWithContext(ctx context.Context, d time.Duration) error {
+	timer := time.NewTimer(d)
+	defer timer.Stop()
+
+	select {
+	case <-timer.C:
+		return nil
+	case <-ctx.Done():
+		return ctx.Err()
+	}
+}
diff --git a/services/rate_limit_test.go b/services/rate_limit_test.go
new file mode 100644
index 0000000..ead08f9
--- /dev/null
+++ b/services/rate_limit_test.go
@@ -0,0 +1,388 @@
+package services
+
+import (
+	"context"
+	"fmt"
+	"net/http"
+	"strconv"
+	"testing"
+	"time"
+)
+
+// mockTransport is a configurable http.RoundTripper for testing.
+type mockTransport struct {
+	handler func(req *http.Request) (*http.Response, error)
+	calls   int
+}
+
+func (m *mockTransport) RoundTrip(req *http.Request) (*http.Response, error) {
+	m.calls++
+	return m.handler(req)
+}
+
+func TestRateLimitTransport_RecordsRateLimitHeaders(t *testing.T) {
+	// Save and restore global state
+	origRemaining, origReset := GlobalRateLimitState.Get()
+	defer GlobalRateLimitState.update(origRemaining, origReset)
+
+	resetTime := time.Now().Add(30 * time.Minute).Unix()
+
+	mock := &mockTransport{
+		handler: func(req *http.Request) (*http.Response, error) {
+			return &http.Response{
+				StatusCode: 200,
+				Header: http.Header{
+					"X-Ratelimit-Remaining": []string{"4500"},
+					"X-Ratelimit-Reset":     []string{strconv.FormatInt(resetTime, 10)},
+				},
+				Body: http.NoBody,
+			}, nil
+		},
+	}
+
+	rt := newRateLimitTransport(mock, nil)
+	req, _ := http.NewRequest("GET", "https://api.github.com/repos", nil)
+	_, err := rt.RoundTrip(req)
+	if err != nil {
+		t.Fatalf("RoundTrip error: %v", err)
+	}
+
+	remaining, reset := GlobalRateLimitState.Get()
+	if remaining != 4500 {
+		t.Errorf("expected remaining=4500, got %d", remaining)
+	}
+	if reset.Unix() != resetTime {
+		t.Errorf("expected resetAt=%d, got %d", resetTime, reset.Unix())
+	}
+}
+
+func TestRateLimitTransport_RetriesOn429(t *testing.T) {
+	callCount := 0
+	mock := &mockTransport{
+		handler: func(req *http.Request) (*http.Response, error) {
+			callCount++
+			if callCount == 1 {
+				return &http.Response{
+					StatusCode: 429,
+					Header: http.Header{
+						"Retry-After": []string{"1"},
+					},
+					Body: http.NoBody,
+				}, nil
+			}
+			return &http.Response{
+				StatusCode: 200,
+				Header:     http.Header{},
+				Body:       http.NoBody,
+			}, nil
+		},
+	}
+
+	rt := newRateLimitTransport(mock, nil)
+	req, _ := http.NewRequest("GET", "https://api.github.com/repos", nil)
+	resp, err := rt.RoundTrip(req)
+	if err != nil {
+		t.Fatalf("RoundTrip error: %v", err)
+	}
+
+	if resp.StatusCode != 200 {
+		t.Errorf("expected status 200 after retry, got %d", resp.StatusCode)
+	}
+	if callCount != 2 {
+		t.Errorf("expected 2 calls (original + retry), got %d", callCount)
+	}
+}
+
+func TestRateLimitTransport_RetriesOn403WithRateLimitExhausted(t *testing.T) {
+	resetTime := time.Now().Add(1 * time.Second).Unix()
+	callCount := 0
+
+	mock := &mockTransport{
+		handler: func(req *http.Request) (*http.Response, error) {
+			callCount++
+			if callCount == 1 {
+				return &http.Response{
+					StatusCode: 403,
+					Header: http.Header{
+						"X-Ratelimit-Remaining": []string{"0"},
+						"X-Ratelimit-Reset":     []string{strconv.FormatInt(resetTime, 10)},
+					},
+					Body: http.NoBody,
+				}, nil
+			}
+			return &http.Response{
+				StatusCode: 200,
+				Header:     http.Header{},
+				Body:       http.NoBody,
+			}, nil
+		},
+	}
+
+	rt := newRateLimitTransport(mock, nil)
+	req, _ := http.NewRequest("GET", "https://api.github.com/repos", nil)
+	resp, err := rt.RoundTrip(req)
+	if err != nil {
+		t.Fatalf("RoundTrip error: %v", err)
+	}
+
+	if resp.StatusCode != 200 {
+		t.Errorf("expected status 200 after retry, got %d", resp.StatusCode)
+	}
+	if callCount != 2 {
+		t.Errorf("expected 2 calls, got %d", callCount)
+	}
+}
+
+func TestRateLimitTransport_NoRetryOnRegular403(t *testing.T) {
+	mock := &mockTransport{
+		handler: func(req *http.Request) (*http.Response, error) {
+			return &http.Response{
+				StatusCode: 403,
+				Header: http.Header{
+					"X-Ratelimit-Remaining": []string{"4999"}, // Not exhausted
+				},
+				Body: http.NoBody,
+			}, nil
+		},
+	}
+
+	rt := newRateLimitTransport(mock, nil)
+	req, _ := http.NewRequest("GET", "https://api.github.com/repos", nil)
+	resp, err := rt.RoundTrip(req)
+	if err != nil {
+		t.Fatalf("RoundTrip error: %v", err)
+	}
+
+	if resp.StatusCode != 403 {
+		t.Errorf("expected status 403 (no retry), got %d", resp.StatusCode)
+	}
+	if mock.calls != 1 {
+		t.Errorf("expected 1 call (no retry), got %d", mock.calls)
+	}
+}
+
+func TestRateLimitTransport_RespectsContextCancellation(t *testing.T) {
+	mock := &mockTransport{
+		handler: func(req *http.Request) (*http.Response, error) {
+			return &http.Response{
+				StatusCode: 429,
+				Header: http.Header{
+					"Retry-After": []string{"60"}, // 60 seconds
+				},
+				Body: http.NoBody,
+			}, nil
+		},
+	}
+
+	rt := newRateLimitTransport(mock, nil)
+
+	ctx, cancel := context.WithTimeout(context.Background(), 100*time.Millisecond)
+	defer cancel()
+
+	req, _ := http.NewRequestWithContext(ctx, "GET", "https://api.github.com/repos", nil)
+	resp, err := rt.RoundTrip(req)
+	if err != nil {
+		t.Fatalf("RoundTrip error: %v", err)
+	}
+
+	// Should return the original 429 response since context cancelled during wait
+	if resp.StatusCode != 429 {
+		t.Errorf("expected original 429 response, got %d", resp.StatusCode)
+	}
+	// Should not have retried (only 1 call to mock)
+	if mock.calls != 1 {
+		t.Errorf("expected 1 call (no retry due to context), got %d", mock.calls)
+	}
+}
+
+func TestRateLimitTransport_RecordsMetrics(t *testing.T) {
+	mc := NewMetricsCollector()
+
+	mock := &mockTransport{
+		handler: func(req *http.Request) (*http.Response, error) {
+			return &http.Response{
+				StatusCode: 200,
+				Header:     http.Header{},
+				Body:       http.NoBody,
+			}, nil
+		},
+	}
+
+	rt := newRateLimitTransport(mock, mc)
+	req, _ := http.NewRequest("GET", "https://api.github.com/repos", nil)
+	_, _ = rt.RoundTrip(req)
+
+	mc.mu.RLock()
+	defer mc.mu.RUnlock()
+	if mc.githubAPICalls != 1 {
+		t.Errorf("expected 1 API call recorded, got %d", mc.githubAPICalls)
+	}
+	if mc.githubAPIErrors != 0 {
+		t.Errorf("expected 0 API errors, got %d", mc.githubAPIErrors)
+	}
+}
+
+func TestRateLimitTransport_RecordsErrorMetrics(t *testing.T) {
+	mc := NewMetricsCollector()
+
+	mock := &mockTransport{
+		handler: func(req *http.Request) (*http.Response, error) {
+			return nil, fmt.Errorf("connection refused")
+		},
+	}
+
+	rt := newRateLimitTransport(mock, mc)
+	req, _ := http.NewRequest("GET", "https://api.github.com/repos", nil)
+	_, _ = rt.RoundTrip(req)
+
+	mc.mu.RLock()
+	defer mc.mu.RUnlock()
+	if mc.githubAPICalls != 1 {
+		t.Errorf("expected 1 API call recorded, got %d", mc.githubAPICalls)
+	}
+	if mc.githubAPIErrors != 1 {
+		t.Errorf("expected 1 API error, got %d", mc.githubAPIErrors)
+	}
+}
+
+func TestIsRateLimited(t *testing.T) {
+	tests := []struct {
+		name       string
+		statusCode int
+		headers    http.Header
+		want       bool
+	}{
+		{
+			name:       "429 is always rate limited",
+			statusCode: 429,
+			headers:    http.Header{},
+			want:       true,
+		},
+		{
+			name:       "403 with remaining 0",
+			statusCode: 403,
+			headers:    http.Header{"X-Ratelimit-Remaining": []string{"0"}},
+			want:       true,
+		},
+		{
+			name:       "403 with Retry-After",
+			statusCode: 403,
+			headers:    http.Header{"Retry-After": []string{"60"}},
+			want:       true,
+		},
+		{
+			name:       "403 with remaining > 0 (not rate limited)",
+			statusCode: 403,
+			headers:    http.Header{"X-Ratelimit-Remaining": []string{"4999"}},
+			want:       false,
+		},
+		{
+			name:       "200 is never rate limited",
+			statusCode: 200,
+			headers:    http.Header{},
+			want:       false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			resp := &http.Response{StatusCode: tt.statusCode, Header: tt.headers}
+			if got := isRateLimited(resp); got != tt.want {
+				t.Errorf("isRateLimited() = %v, want %v", got, tt.want)
+			}
+		})
+	}
+}
+
+func TestRetryAfterDuration(t *testing.T) {
+	tests := []struct {
+		name    string
+		headers http.Header
+		wantMin time.Duration
+		wantMax time.Duration
+	}{
+		{
+			name:    "Retry-After in seconds",
+			headers: http.Header{"Retry-After": []string{"5"}},
+			wantMin: 5 * time.Second,
+			wantMax: 5 * time.Second,
+		},
+		{
+			name:    "Retry-After capped at 60s",
+			headers: http.Header{"Retry-After": []string{"120"}},
+			wantMin: 60 * time.Second,
+			wantMax: 60 * time.Second,
+		},
+		{
+			name: "X-RateLimit-Reset fallback",
+			headers: http.Header{
+				"X-Ratelimit-Reset": []string{strconv.FormatInt(time.Now().Add(10*time.Second).Unix(), 10)},
+			},
+			wantMin: 8 * time.Second,  // Allow some clock skew
+			wantMax: 12 * time.Second, // Allow some clock skew
+		},
+		{
+			name:    "no headers returns 0",
+			headers: http.Header{},
+			wantMin: 0,
+			wantMax: 0,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			resp := &http.Response{Header: tt.headers}
+			got := retryAfterDuration(resp)
+			if got < tt.wantMin || got > tt.wantMax {
+				t.Errorf("retryAfterDuration() = %v, want between %v and %v", got, tt.wantMin, tt.wantMax)
+			}
+		})
+	}
+}
+
+func TestRateLimitState_Concurrent(t *testing.T) {
+	state := &RateLimitState{remaining: -1}
+
+	done := make(chan struct{})
+	go func() {
+		for i := 0; i < 1000; i++ {
+			state.update(i, time.Now())
+		}
+		close(done)
+	}()
+
+	// Concurrent reads while writing
+	for i := 0; i < 1000; i++ {
+		state.Get()
+	}
+
+	<-done // Wait for writer to finish
+}
+
+func TestCurrentRateLimitInfo_DefaultState(t *testing.T) {
+	// Save and restore
+	origRemaining, origReset := GlobalRateLimitState.Get()
+	defer GlobalRateLimitState.update(origRemaining, origReset)
+
+	GlobalRateLimitState.update(-1, time.Time{})
+	info := currentRateLimitInfo()
+	if info.Remaining != -1 {
+		t.Errorf("expected remaining=-1 for default state, got %d", info.Remaining)
+	}
+}
+
+func TestCurrentRateLimitInfo_WithData(t *testing.T) {
+	origRemaining, origReset := GlobalRateLimitState.Get()
+	defer GlobalRateLimitState.update(origRemaining, origReset)
+
+	resetAt := time.Now().Add(30 * time.Minute)
+	GlobalRateLimitState.update(4500, resetAt)
+
+	info := currentRateLimitInfo()
+	if info.Remaining != 4500 {
+		t.Errorf("expected remaining=4500, got %d", info.Remaining)
+	}
+	if info.ResetAt.Unix() != resetAt.Unix() {
+		t.Errorf("expected resetAt=%v, got %v", resetAt, info.ResetAt)
+	}
+}
diff --git a/services/service_container.go b/services/service_container.go
index e9b6879..62d6e2b 100644
--- a/services/service_container.go
+++ b/services/service_container.go
@@ -13,6 +13,7 @@ import (
 type ServiceContainer struct {
 	Config           *configs.Config
 	FileStateService FileStateService
+	TokenManager     *TokenManager
 
 	// New services
 	ConfigLoader      ConfigLoader
@@ -24,9 +25,15 @@ type ServiceContainer struct {
 	MetricsCollector  *MetricsCollector
 	SlackNotifier     SlackNotifier
 
+	// Webhook deduplication
+	DeliveryTracker *DeliveryTracker
+
 	// Server state
 	StartTime time.Time
 
+	// Background goroutine tracking (for graceful shutdown and tests)
+	wg sync.WaitGroup
+
 	// Shutdown state
 	closeOnce sync.Once
 	closed    bool
@@ -77,6 +84,7 @@ func NewServiceContainer(config *configs.Config) (*ServiceContainer, error) {
 	return &ServiceContainer{
 		Config:            config,
 		FileStateService:  fileStateService,
+		TokenManager:      defaultTokenManager,
 		ConfigLoader:      configLoader,
 		PatternMatcher:    patternMatcher,
 		PathTransformer:   pathTransformer,
@@ -85,14 +93,23 @@ func NewServiceContainer(config *configs.Config) (*ServiceContainer, error) {
 		AuditLogger:       auditLogger,
 		MetricsCollector:  metricsCollector,
 		SlackNotifier:     slackNotifier,
+		DeliveryTracker:   NewDeliveryTracker(1 * time.Hour),
 		StartTime:         time.Now(),
 	}, nil
 }
 
+// Wait blocks until all background goroutines tracked by this container have finished.
+func (sc *ServiceContainer) Wait() {
+	sc.wg.Wait()
+}
+
 // Close cleans up resources. Safe to call multiple times.
 func (sc *ServiceContainer) Close(ctx context.Context) error {
 	var closeErr error
 	sc.closeOnce.Do(func() {
+		if sc.DeliveryTracker != nil {
+			sc.DeliveryTracker.Stop()
+		}
 		if sc.AuditLogger != nil {
 			closeErr = sc.AuditLogger.Close(ctx)
 		}
diff --git a/services/service_container_test.go b/services/service_container_test.go
index ed8bcc7..96cebbc 100644
--- a/services/service_container_test.go
+++ b/services/service_container_test.go
@@ -110,6 +110,10 @@ func TestNewServiceContainer(t *testing.T) {
 					t.Error("SlackNotifier is nil")
 				}
 
+				if container.TokenManager == nil {
+					t.Error("TokenManager is nil")
+				}
+
 				// Check that StartTime is set
 				if container.StartTime.IsZero() {
 					t.Error("StartTime is zero")
diff --git a/services/slack_notifier.go b/services/slack_notifier.go
index c1614d8..bb6eccb 100644
--- a/services/slack_notifier.go
+++ b/services/slack_notifier.go
@@ -13,57 +13,57 @@ import (
 type SlackNotifier interface {
 	// NotifyPRProcessed sends a notification when a PR is successfully processed
 	NotifyPRProcessed(ctx context.Context, event *PRProcessedEvent) error
-	
+
 	// NotifyError sends a notification when an error occurs
 	NotifyError(ctx context.Context, event *ErrorEvent) error
-	
+
 	// NotifyFilesCopied sends a notification when files are copied
 	NotifyFilesCopied(ctx context.Context, event *FilesCopiedEvent) error
-	
+
 	// NotifyDeprecation sends a notification when files are deprecated
 	NotifyDeprecation(ctx context.Context, event *DeprecationEvent) error
-	
+
 	// IsEnabled returns true if Slack notifications are enabled
 	IsEnabled() bool
 }
 
 // PRProcessedEvent contains information about a processed PR
 type PRProcessedEvent struct {
-	PRNumber      int
-	PRTitle       string
-	PRURL         string
-	SourceRepo    string
-	FilesMatched  int
-	FilesCopied   int
-	FilesFailed   int
+	PRNumber       int
+	PRTitle        string
+	PRURL          string
+	SourceRepo     string
+	FilesMatched   int
+	FilesCopied    int
+	FilesFailed    int
 	ProcessingTime time.Duration
 }
 
 // ErrorEvent contains information about an error
 type ErrorEvent struct {
-	Operation   string
-	Error       error
-	PRNumber    int
-	SourceRepo  string
+	Operation      string
+	Error          error
+	PRNumber       int
+	SourceRepo     string
 	AdditionalInfo map[string]interface{}
 }
 
 // FilesCopiedEvent contains information about copied files
 type FilesCopiedEvent struct {
-	PRNumber    int
-	SourceRepo  string
-	TargetRepo  string
-	FileCount   int
-	Files       []string
-	RuleName    string
+	PRNumber   int
+	SourceRepo string
+	TargetRepo string
+	FileCount  int
+	Files      []string
+	RuleName   string
 }
 
 // DeprecationEvent contains information about deprecated files
 type DeprecationEvent struct {
-	PRNumber    int
-	SourceRepo  string
-	FileCount   int
-	Files       []string
+	PRNumber   int
+	SourceRepo string
+	FileCount  int
+	Files      []string
 }
 
 // DefaultSlackNotifier implements SlackNotifier using Slack webhooks
@@ -79,7 +79,7 @@ type DefaultSlackNotifier struct {
 // NewSlackNotifier creates a new Slack notifier
 func NewSlackNotifier(webhookURL, channel, username, iconEmoji string) SlackNotifier {
 	enabled := webhookURL != ""
-	
+
 	return &DefaultSlackNotifier{
 		webhookURL: webhookURL,
 		enabled:    enabled,
@@ -102,22 +102,22 @@ func (sn *DefaultSlackNotifier) NotifyPRProcessed(ctx context.Context, event *PR
 	if !sn.enabled {
 		return nil
 	}
-	
+
 	color := "good" // green
 	if event.FilesFailed > 0 {
 		color = "warning" // yellow
 	}
-	
+
 	message := &SlackMessage{
 		Channel:   sn.channel,
 		Username:  sn.username,
 		IconEmoji: sn.iconEmoji,
 		Attachments: []SlackAttachment{
 			{
-				Color:      color,
-				Title:      fmt.Sprintf("✅ PR #%d Processed", event.PRNumber),
-				TitleLink:  event.PRURL,
-				Text:       event.PRTitle,
+				Color:     color,
+				Title:     fmt.Sprintf("✅ PR #%d Processed", event.PRNumber),
+				TitleLink: event.PRURL,
+				Text:      event.PRTitle,
 				Fields: []SlackField{
 					{Title: "Repository", Value: event.SourceRepo, Short: true},
 					{Title: "Files Matched", Value: fmt.Sprintf("%d", event.FilesMatched), Short: true},
@@ -131,7 +131,7 @@ func (sn *DefaultSlackNotifier) NotifyPRProcessed(ctx context.Context, event *PR
 			},
 		},
 	}
-	
+
 	return sn.sendMessage(ctx, message)
 }
 
@@ -140,20 +140,20 @@ func (sn *DefaultSlackNotifier) NotifyError(ctx context.Context, event *ErrorEve
 	if !sn.enabled {
 		return nil
 	}
-	
+
 	fields := []SlackField{
 		{Title: "Operation", Value: event.Operation, Short: true},
 		{Title: "Error", Value: event.Error.Error(), Short: false},
 	}
-	
+
 	if event.SourceRepo != "" {
 		fields = append(fields, SlackField{Title: "Repository", Value: event.SourceRepo, Short: true})
 	}
-	
+
 	if event.PRNumber > 0 {
 		fields = append(fields, SlackField{Title: "PR Number", Value: fmt.Sprintf("#%d", event.PRNumber), Short: true})
 	}
-	
+
 	message := &SlackMessage{
 		Channel:   sn.channel,
 		Username:  sn.username,
@@ -170,7 +170,7 @@ func (sn *DefaultSlackNotifier) NotifyError(ctx context.Context, event *ErrorEve
 			},
 		},
 	}
-	
+
 	return sn.sendMessage(ctx, message)
 }
 
@@ -179,28 +179,28 @@ func (sn *DefaultSlackNotifier) NotifyFilesCopied(ctx context.Context, event *Fi
 	if !sn.enabled {
 		return nil
 	}
-	
+
 	// Limit files shown to first 10
 	filesText := ""
 	displayFiles := event.Files
 	if len(displayFiles) > 10 {
 		displayFiles = displayFiles[:10]
-		filesText = fmt.Sprintf("```\n%s\n... and %d more```", 
-			formatFileList(displayFiles), 
+		filesText = fmt.Sprintf("```\n%s\n... and %d more```",
+			formatFileList(displayFiles),
 			len(event.Files)-10)
 	} else {
 		filesText = fmt.Sprintf("```\n%s```", formatFileList(displayFiles))
 	}
-	
+
 	message := &SlackMessage{
 		Channel:   sn.channel,
 		Username:  sn.username,
 		IconEmoji: sn.iconEmoji,
 		Attachments: []SlackAttachment{
 			{
-				Color:      "good", // green
-				Title:      fmt.Sprintf("📋 Files Copied from PR #%d", event.PRNumber),
-				Text:       filesText,
+				Color: "good", // green
+				Title: fmt.Sprintf("📋 Files Copied from PR #%d", event.PRNumber),
+				Text:  filesText,
 				Fields: []SlackField{
 					{Title: "Source", Value: event.SourceRepo, Short: true},
 					{Title: "Target", Value: event.TargetRepo, Short: true},
@@ -213,7 +213,7 @@ func (sn *DefaultSlackNotifier) NotifyFilesCopied(ctx context.Context, event *Fi
 			},
 		},
 	}
-	
+
 	return sn.sendMessage(ctx, message)
 }
 
@@ -222,18 +222,18 @@ func (sn *DefaultSlackNotifier) NotifyDeprecation(ctx context.Context, event *De
 	if !sn.enabled {
 		return nil
 	}
-	
+
 	filesText := fmt.Sprintf("```\n%s```", formatFileList(event.Files))
-	
+
 	message := &SlackMessage{
 		Channel:   sn.channel,
 		Username:  sn.username,
 		IconEmoji: sn.iconEmoji,
 		Attachments: []SlackAttachment{
 			{
-				Color:      "warning", // yellow
-				Title:      fmt.Sprintf("⚠️ Files Deprecated from PR #%d", event.PRNumber),
-				Text:       filesText,
+				Color: "warning", // yellow
+				Title: fmt.Sprintf("⚠️ Files Deprecated from PR #%d", event.PRNumber),
+				Text:  filesText,
 				Fields: []SlackField{
 					{Title: "Repository", Value: event.SourceRepo, Short: true},
 					{Title: "File Count", Value: fmt.Sprintf("%d", event.FileCount), Short: true},
@@ -244,7 +244,7 @@ func (sn *DefaultSlackNotifier) NotifyDeprecation(ctx context.Context, event *De
 			},
 		},
 	}
-	
+
 	return sn.sendMessage(ctx, message)
 }
 
@@ -254,24 +254,24 @@ func (sn *DefaultSlackNotifier) sendMessage(ctx context.Context, message *SlackM
 	if err != nil {
 		return fmt.Errorf("failed to marshal slack message: %w", err)
 	}
-	
+
 	req, err := http.NewRequestWithContext(ctx, "POST", sn.webhookURL, bytes.NewBuffer(payload))
 	if err != nil {
 		return fmt.Errorf("failed to create slack request: %w", err)
 	}
-	
+
 	req.Header.Set("Content-Type", "application/json")
-	
+
 	resp, err := sn.httpClient.Do(req)
 	if err != nil {
 		return fmt.Errorf("failed to send slack message: %w", err)
 	}
-	defer resp.Body.Close()
-	
+	defer func() { _ = resp.Body.Close() }()
+
 	if resp.StatusCode != http.StatusOK {
 		return fmt.Errorf("slack returned non-200 status: %d", resp.StatusCode)
 	}
-	
+
 	return nil
 }
 
@@ -286,11 +286,11 @@ func formatFileList(files []string) string {
 
 // SlackMessage represents a Slack message
 type SlackMessage struct {
-	Channel     string             `json:"channel,omitempty"`
-	Username    string             `json:"username,omitempty"`
-	IconEmoji   string             `json:"icon_emoji,omitempty"`
-	Text        string             `json:"text,omitempty"`
-	Attachments []SlackAttachment  `json:"attachments,omitempty"`
+	Channel     string            `json:"channel,omitempty"`
+	Username    string            `json:"username,omitempty"`
+	IconEmoji   string            `json:"icon_emoji,omitempty"`
+	Text        string            `json:"text,omitempty"`
+	Attachments []SlackAttachment `json:"attachments,omitempty"`
 }
 
 // SlackAttachment represents a Slack message attachment
@@ -311,4 +311,3 @@ type SlackField struct {
 	Value string `json:"value"`
 	Short bool   `json:"short"`
 }
-
diff --git a/services/token_manager.go b/services/token_manager.go
new file mode 100644
index 0000000..0280d6e
--- /dev/null
+++ b/services/token_manager.go
@@ -0,0 +1,134 @@
+package services
+
+import (
+	"net/http"
+	"sync"
+	"time"
+)
+
+// tokenEntry stores a cached installation token with its expiration time.
+type tokenEntry struct {
+	Token     string
+	ExpiresAt time.Time
+}
+
+// TokenManager provides thread-safe management of GitHub App authentication tokens.
+// It caches JWT tokens and per-org installation tokens with expiry tracking,
+// and holds the HTTP client used for GitHub API calls.
+type TokenManager struct {
+	mu sync.RWMutex
+
+	// Default installation access token (set once at startup via ConfigurePermissions)
+	installationAccessToken string
+
+	// Per-org installation token cache with expiry
+	installationTokenCache map[string]tokenEntry
+
+	// Cached JWT token and its expiry
+	cachedJWT       string
+	cachedJWTExpiry time.Time
+
+	// HTTP client used for GitHub API calls (swappable for testing with httpmock)
+	httpClient *http.Client
+}
+
+// NewTokenManager creates a new TokenManager instance.
+func NewTokenManager() *TokenManager {
+	return &TokenManager{
+		installationTokenCache: make(map[string]tokenEntry),
+		httpClient:             http.DefaultClient,
+	}
+}
+
+// GetInstallationAccessToken returns the default installation access token.
+func (tm *TokenManager) GetInstallationAccessToken() string {
+	tm.mu.RLock()
+	defer tm.mu.RUnlock()
+	return tm.installationAccessToken
+}
+
+// SetInstallationAccessToken sets the default installation access token.
+func (tm *TokenManager) SetInstallationAccessToken(token string) {
+	tm.mu.Lock()
+	defer tm.mu.Unlock()
+	tm.installationAccessToken = token
+}
+
+// GetHTTPClient returns the HTTP client used for GitHub API calls.
+func (tm *TokenManager) GetHTTPClient() *http.Client {
+	tm.mu.RLock()
+	defer tm.mu.RUnlock()
+	if tm.httpClient == nil {
+		return http.DefaultClient
+	}
+	return tm.httpClient
+}
+
+// SetHTTPClient sets the HTTP client used for GitHub API calls.
+func (tm *TokenManager) SetHTTPClient(client *http.Client) {
+	tm.mu.Lock()
+	defer tm.mu.Unlock()
+	tm.httpClient = client
+}
+
+// GetTokenForOrg returns a cached token for the given org if it exists and is still valid.
+// Returns empty string and false if no valid token exists.
+func (tm *TokenManager) GetTokenForOrg(org string) (string, bool) {
+	tm.mu.RLock()
+	defer tm.mu.RUnlock()
+	entry, ok := tm.installationTokenCache[org]
+	if !ok || entry.Token == "" {
+		return "", false
+	}
+	// Check if token is expired (with 5-minute buffer for safety)
+	if !entry.ExpiresAt.IsZero() && time.Now().After(entry.ExpiresAt.Add(-5*time.Minute)) {
+		return "", false
+	}
+	return entry.Token, true
+}
+
+// SetTokenForOrg caches an installation token for an org with expiry.
+func (tm *TokenManager) SetTokenForOrg(org, token string, expiresAt time.Time) {
+	tm.mu.Lock()
+	defer tm.mu.Unlock()
+	tm.installationTokenCache[org] = tokenEntry{
+		Token:     token,
+		ExpiresAt: expiresAt,
+	}
+}
+
+// SetTokenForOrgNoExpiry caches an installation token for an org without expiry tracking.
+// Primarily used in tests where token expiry is not relevant.
+func (tm *TokenManager) SetTokenForOrgNoExpiry(org, token string) {
+	tm.mu.Lock()
+	defer tm.mu.Unlock()
+	tm.installationTokenCache[org] = tokenEntry{
+		Token: token,
+	}
+}
+
+// GetCachedJWT returns the cached JWT if it's still valid.
+func (tm *TokenManager) GetCachedJWT() (string, bool) {
+	tm.mu.RLock()
+	defer tm.mu.RUnlock()
+	if tm.cachedJWT != "" && time.Now().Before(tm.cachedJWTExpiry) {
+		return tm.cachedJWT, true
+	}
+	return "", false
+}
+
+// SetCachedJWT caches a JWT with its expiry time.
+func (tm *TokenManager) SetCachedJWT(token string, expiry time.Time) {
+	tm.mu.Lock()
+	defer tm.mu.Unlock()
+	tm.cachedJWT = token
+	tm.cachedJWTExpiry = expiry
+}
+
+// defaultTokenManager is the package-level TokenManager instance.
+var defaultTokenManager = NewTokenManager()
+
+// DefaultTokenManager returns the package-level TokenManager instance.
+func DefaultTokenManager() *TokenManager {
+	return defaultTokenManager
+}
diff --git a/services/webhook_handler_new.go b/services/webhook_handler_new.go
index dd7ec04..234ac2d 100644
--- a/services/webhook_handler_new.go
+++ b/services/webhook_handler_new.go
@@ -11,7 +11,7 @@ import (
 	"strings"
 	"time"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/configs"
 	"github.com/grove-platform/github-copier/types"
 )
@@ -44,8 +44,12 @@ func simpleVerifySignature(sigHeader string, body, secret []byte) bool {
 }
 
 // RetrieveFileContentsWithConfigAndBranch fetches file contents from a specific branch
-func RetrieveFileContentsWithConfigAndBranch(ctx context.Context, filePath string, branch string, repoOwner string, repoName string) (*github.RepositoryContent, error) {
-	client := GetRestClient()
+func RetrieveFileContentsWithConfigAndBranch(ctx context.Context, config *configs.Config, filePath string, branch string, repoOwner string, repoName string) (*github.RepositoryContent, error) {
+	// Use org-specific client to ensure we have the right installation token
+	client, err := GetRestClientForOrg(ctx, config, repoOwner)
+	if err != nil {
+		return nil, fmt.Errorf("failed to get GitHub client for org %s: %w", repoOwner, err)
+	}
 
 	fileContent, _, _, err := client.Repositories.GetContents(
 		ctx,
@@ -65,6 +69,12 @@ func RetrieveFileContentsWithConfigAndBranch(ctx context.Context, filePath strin
 
 // HandleWebhookWithContainer handles incoming GitHub webhook requests using the service container
 func HandleWebhookWithContainer(w http.ResponseWriter, r *http.Request, config *configs.Config, container *ServiceContainer) {
+	// GitHub webhooks are always POST
+	if r.Method != http.MethodPost {
+		http.Error(w, "method not allowed", http.StatusMethodNotAllowed)
+		return
+	}
+
 	startTime := time.Now()
 	ctx := r.Context()
 
@@ -90,9 +100,23 @@ func HandleWebhookWithContainer(w http.ResponseWriter, r *http.Request, config *
 		return
 	}
 
+	// Check for duplicate delivery using X-GitHub-Delivery header
+	deliveryID := r.Header.Get("X-GitHub-Delivery")
+	if deliveryID != "" && container.DeliveryTracker != nil {
+		if !container.DeliveryTracker.TryRecord(deliveryID) {
+			LogInfoCtx(ctx, "duplicate webhook delivery, skipping", map[string]interface{}{
+				"delivery_id": deliveryID,
+				"event_type":  eventType,
+			})
+			w.WriteHeader(http.StatusOK)
+			return
+		}
+	}
+
 	LogInfoCtx(ctx, "payload read", map[string]interface{}{
-		"elapsed_ms": time.Since(startTime).Milliseconds(),
-		"size_bytes": len(payload),
+		"elapsed_ms":  time.Since(startTime).Milliseconds(),
+		"size_bytes":  len(payload),
+		"delivery_id": deliveryID,
 	})
 
 	// Verify webhook signature
@@ -107,6 +131,8 @@ func HandleWebhookWithContainer(w http.ResponseWriter, r *http.Request, config *
 		LogInfoCtx(ctx, "signature verified", map[string]interface{}{
 			"elapsed_ms": time.Since(startTime).Milliseconds(),
 		})
+	} else {
+		LogWarningCtx(ctx, "webhook signature verification DISABLED - no webhook secret configured; set WEBHOOK_SECRET for production use", nil)
 	}
 
 	// Parse webhook event
@@ -142,7 +168,7 @@ func HandleWebhookWithContainer(w http.ResponseWriter, r *http.Request, config *
 		"merged": merged,
 	})
 
-	if !(action == "closed" && merged) {
+	if action != "closed" || !merged {
 		LogInfoCtx(ctx, "skipping non-merged PR", map[string]interface{}{
 			"action": action,
 			"merged": merged,
@@ -174,6 +200,7 @@ func HandleWebhookWithContainer(w http.ResponseWriter, r *http.Request, config *
 		"sha":         sourceCommitSHA,
 		"repo":        fmt.Sprintf("%s/%s", repoOwner, repoName),
 		"base_branch": baseBranch,
+		"delivery_id": deliveryID,
 		"elapsed_ms":  time.Since(startTime).Milliseconds(),
 	})
 
@@ -184,7 +211,9 @@ func HandleWebhookWithContainer(w http.ResponseWriter, r *http.Request, config *
 
 	w.Header().Set("Content-Type", "application/json")
 	w.WriteHeader(http.StatusAccepted)
-	_, _ = w.Write([]byte(`{"status":"accepted"}`))
+	if _, err := w.Write([]byte(`{"status":"accepted"}`)); err != nil {
+		LogWarningCtx(ctx, "failed to write webhook response body", map[string]interface{}{"error": err.Error()})
+	}
 
 	LogInfoCtx(ctx, "response sent", map[string]interface{}{
 		"elapsed_ms": time.Since(startTime).Milliseconds(),
@@ -201,122 +230,150 @@ func HandleWebhookWithContainer(w http.ResponseWriter, r *http.Request, config *
 	// Process asynchronously in background with a new context
 	// Don't use the request context as it will be cancelled when the request completes
 	bgCtx := context.Background()
-	go handleMergedPRWithContainer(bgCtx, prNumber, sourceCommitSHA, repoOwner, repoName, baseBranch, config, container)
+	container.wg.Add(1)
+	go func() {
+		defer container.wg.Done()
+		defer func() {
+			if r := recover(); r != nil {
+				LogCritical("panic in webhook handler", "pr_number", prNumber, "repo_owner", repoOwner, "repo_name", repoName, "recovered", r)
+				container.MetricsCollector.RecordWebhookFailed()
+				if notifyErr := container.SlackNotifier.NotifyError(bgCtx, &ErrorEvent{
+					Operation:  "panic_recovery",
+					Error:      fmt.Errorf("panic: %v", r),
+					PRNumber:   prNumber,
+					SourceRepo: fmt.Sprintf("%s/%s", repoOwner, repoName),
+				}); notifyErr != nil {
+					LogWarning("failed to send Slack error notification", "error", notifyErr)
+				}
+			}
+		}()
+		handleMergedPRWithContainer(bgCtx, prNumber, sourceCommitSHA, repoOwner, repoName, baseBranch, config, container)
+	}()
 }
 
-// handleMergedPRWithContainer processes a merged PR using the new pattern matching system
+// handleMergedPRWithContainer orchestrates processing of a merged PR:
+// auth → config → match workflows → fetch changed files → process → upload → notify.
 func handleMergedPRWithContainer(ctx context.Context, prNumber int, sourceCommitSHA string, repoOwner string, repoName string, baseBranch string, config *configs.Config, container *ServiceContainer) {
 	startTime := time.Now()
+	webhookRepo := fmt.Sprintf("%s/%s", repoOwner, repoName)
 
-	// Configure GitHub permissions
-	if InstallationAccessToken == "" {
-		if err := ConfigurePermissions(); err != nil {
+	// 1. Ensure GitHub auth
+	if defaultTokenManager.GetInstallationAccessToken() == "" {
+		if err := ConfigurePermissions(ctx, config); err != nil {
 			LogAndReturnError(ctx, "auth", "failed to configure GitHub permissions", err)
 			container.MetricsCollector.RecordWebhookFailed()
 			return
 		}
 	}
 
-	// Load configuration using new loader
-	// Note: config.ConfigRepoOwner and config.ConfigRepoName are already set from env.yaml
-	// The webhook repoOwner/repoName are used for matching workflows, not for loading config
+	// 2. Load config and find matching workflows
+	yamlConfig, err := loadAndMatchWorkflows(ctx, config, container, webhookRepo, baseBranch, prNumber)
+	if err != nil {
+		return // already logged and notified
+	}
+
+	// 3. Fetch changed files from the source PR
+	changedFiles, err := fetchChangedFiles(ctx, config, container, repoOwner, repoName, prNumber, webhookRepo)
+	if err != nil {
+		return // already logged and notified
+	}
+
+	// 4. Snapshot metrics before processing
+	filesMatchedBefore := container.MetricsCollector.GetFilesMatched()
+	filesUploadedBefore := container.MetricsCollector.GetFilesUploaded()
+	filesFailedBefore := container.MetricsCollector.GetFilesUploadFailed()
+
+	// 5. Process workflows, upload files, and update deprecations
+	processFilesWithWorkflows(ctx, prNumber, sourceCommitSHA, changedFiles, yamlConfig, config, container)
+	uploadAndDeprecateFiles(ctx, config, container)
+
+	// 6. Report completion
+	reportCompletion(ctx, container, webhookRepo, prNumber, sourceCommitSHA, startTime,
+		filesMatchedBefore, filesUploadedBefore, filesFailedBefore)
+}
+
+// loadAndMatchWorkflows loads the YAML config and filters to workflows matching
+// the webhook's source repo and branch. Returns nil and logs/notifies on error.
+func loadAndMatchWorkflows(ctx context.Context, config *configs.Config, container *ServiceContainer, webhookRepo string, baseBranch string, prNumber int) (*types.YAMLConfig, error) {
 	yamlConfig, err := container.ConfigLoader.LoadConfig(ctx, config)
 	if err != nil {
 		LogAndReturnError(ctx, "config_load", "failed to load config", err)
 		container.MetricsCollector.RecordWebhookFailed()
-
-		// Send error notification to Slack
-		_ = container.SlackNotifier.NotifyError(ctx, &ErrorEvent{
-			Operation:  "config_load",
-			Error:      err,
-			PRNumber:   prNumber,
-			SourceRepo: fmt.Sprintf("%s/%s", repoOwner, repoName),
-		})
-		return
+		notifySlackError(ctx, container, "config_load", err, prNumber, webhookRepo)
+		return nil, err
 	}
 
-	// Find workflows matching this source repo and branch
-	webhookRepo := fmt.Sprintf("%s/%s", repoOwner, repoName)
-	var matchingWorkflows []types.Workflow
-	for _, workflow := range yamlConfig.Workflows {
-		// Match both repository and branch
-		if workflow.Source.Repo == webhookRepo && workflow.Source.Branch == baseBranch {
-			matchingWorkflows = append(matchingWorkflows, workflow)
+	var matching []types.Workflow
+	for _, wf := range yamlConfig.Workflows {
+		if wf.Source.Repo == webhookRepo && wf.Source.Branch == baseBranch {
+			matching = append(matching, wf)
 		}
 	}
 
-	if len(matchingWorkflows) == 0 {
+	if len(matching) == 0 {
 		LogWarningCtx(ctx, "no workflows configured for source repository and branch", map[string]interface{}{
 			"webhook_repo":   webhookRepo,
 			"base_branch":    baseBranch,
 			"workflow_count": len(yamlConfig.Workflows),
 		})
 		container.MetricsCollector.RecordWebhookFailed()
-		return
+		return nil, fmt.Errorf("no matching workflows")
 	}
 
 	LogInfoCtx(ctx, "found matching workflows", map[string]interface{}{
 		"webhook_repo":   webhookRepo,
 		"base_branch":    baseBranch,
-		"matching_count": len(matchingWorkflows),
+		"matching_count": len(matching),
 	})
 
-	// Store matching workflows for processing
-	yamlConfig.Workflows = matchingWorkflows
+	yamlConfig.Workflows = matching
+	return yamlConfig, nil
+}
 
-	// Get changed files from PR (from the source repository that triggered the webhook)
-	changedFiles, err := GetFilesChangedInPr(repoOwner, repoName, prNumber)
+// fetchChangedFiles retrieves the files changed in a PR, logging and notifying on error.
+func fetchChangedFiles(ctx context.Context, config *configs.Config, container *ServiceContainer, repoOwner string, repoName string, prNumber int, webhookRepo string) ([]types.ChangedFile, error) {
+	changedFiles, err := GetFilesChangedInPr(ctx, config, repoOwner, repoName, prNumber)
 	if err != nil {
 		LogAndReturnError(ctx, "get_files", "failed to get changed files", err)
 		container.MetricsCollector.RecordWebhookFailed()
-
-		// Send error notification to Slack
-		_ = container.SlackNotifier.NotifyError(ctx, &ErrorEvent{
-			Operation:  "get_files",
-			Error:      err,
-			PRNumber:   prNumber,
-			SourceRepo: webhookRepo,
-		})
-		return
+		notifySlackError(ctx, container, "get_files", err, prNumber, webhookRepo)
+		return nil, err
 	}
 
 	LogInfoCtx(ctx, "retrieved changed files", map[string]interface{}{
 		"count": len(changedFiles),
 	})
+	return changedFiles, nil
+}
 
-	// Track metrics before processing
-	filesMatchedBefore := container.MetricsCollector.GetFilesMatched()
-	filesUploadedBefore := container.MetricsCollector.GetFilesUploaded()
-	filesFailedBefore := container.MetricsCollector.GetFilesUploadFailed()
-
-	// Process files with workflow processor
-	processFilesWithWorkflows(ctx, prNumber, sourceCommitSHA, changedFiles, yamlConfig, container)
-
+// uploadAndDeprecateFiles drains the file-state queues, uploading files to target
+// repos and updating the deprecation file.
+func uploadAndDeprecateFiles(ctx context.Context, config *configs.Config, container *ServiceContainer) {
 	// Upload queued files
-	FilesToUpload = container.FileStateService.GetFilesToUpload()
-	AddFilesToTargetRepoBranchWithFetcher(container.PRTemplateFetcher, container.MetricsCollector)
+	filesToUpload := container.FileStateService.GetFilesToUpload()
+	AddFilesToTargetRepos(ctx, config, filesToUpload, container.PRTemplateFetcher, container.MetricsCollector)
 	container.FileStateService.ClearFilesToUpload()
 
-	// Update deprecation file - copy from FileStateService to global map for legacy function
-	// The deprecationMap is keyed by deprecation file name, with a slice of entries per file
+	// Build deprecation map and update file
 	deprecationMap := container.FileStateService.GetFilesToDeprecate()
-	FilesToDeprecate = make(map[string]types.Configs)
+	filesToDeprecate := make(map[string]types.Configs)
 	for _, entries := range deprecationMap {
-		// Iterate over all entries for each deprecation file
 		for _, entry := range entries {
-			FilesToDeprecate[entry.FileName] = types.Configs{
+			filesToDeprecate[entry.FileName] = types.Configs{
 				TargetRepo:   entry.Repo,
 				TargetBranch: entry.Branch,
 			}
 		}
 	}
-	UpdateDeprecationFile()
+	UpdateDeprecationFile(ctx, config, filesToDeprecate)
 	container.FileStateService.ClearFilesToDeprecate()
+}
 
-	// Calculate metrics after processing
-	filesMatched := container.MetricsCollector.GetFilesMatched() - filesMatchedBefore
-	filesUploaded := container.MetricsCollector.GetFilesUploaded() - filesUploadedBefore
-	filesFailed := container.MetricsCollector.GetFilesUploadFailed() - filesFailedBefore
+// reportCompletion calculates processing metrics and sends a Slack notification.
+func reportCompletion(ctx context.Context, container *ServiceContainer, webhookRepo string, prNumber int, sourceCommitSHA string, startTime time.Time, matchedBefore int, uploadedBefore int, failedBefore int) {
+	filesMatched := container.MetricsCollector.GetFilesMatched() - matchedBefore
+	filesUploaded := container.MetricsCollector.GetFilesUploaded() - uploadedBefore
+	filesFailed := container.MetricsCollector.GetFilesUploadFailed() - failedBefore
 	processingTime := time.Since(startTime)
 
 	LogInfoCtx(ctx, "--Done--", map[string]interface{}{
@@ -324,22 +381,35 @@ func handleMergedPRWithContainer(ctx context.Context, prNumber int, sourceCommit
 		"sha":       sourceCommitSHA,
 	})
 
-	// Send success notification to Slack
-	_ = container.SlackNotifier.NotifyPRProcessed(ctx, &PRProcessedEvent{
+	if notifyErr := container.SlackNotifier.NotifyPRProcessed(ctx, &PRProcessedEvent{
 		PRNumber:       prNumber,
-		PRTitle:        fmt.Sprintf("PR #%d", prNumber), // TODO: Get actual PR title from GitHub
+		PRTitle:        fmt.Sprintf("PR #%d", prNumber),
 		PRURL:          fmt.Sprintf("https://github.com/%s/pull/%d", webhookRepo, prNumber),
 		SourceRepo:     webhookRepo,
 		FilesMatched:   filesMatched,
 		FilesCopied:    filesUploaded,
 		FilesFailed:    filesFailed,
 		ProcessingTime: processingTime,
-	})
+	}); notifyErr != nil {
+		LogWarningCtx(ctx, "failed to send Slack PR processed notification", map[string]interface{}{"error": notifyErr.Error()})
+	}
+}
+
+// notifySlackError is a helper to send a Slack error notification, logging any failure.
+func notifySlackError(ctx context.Context, container *ServiceContainer, operation string, err error, prNumber int, sourceRepo string) {
+	if notifyErr := container.SlackNotifier.NotifyError(ctx, &ErrorEvent{
+		Operation:  operation,
+		Error:      err,
+		PRNumber:   prNumber,
+		SourceRepo: sourceRepo,
+	}); notifyErr != nil {
+		LogWarningCtx(ctx, "failed to send Slack error notification", map[string]interface{}{"error": notifyErr.Error()})
+	}
 }
 
 // processFilesWithWorkflows processes changed files using the workflow system
 func processFilesWithWorkflows(ctx context.Context, prNumber int, sourceCommitSHA string,
-	changedFiles []types.ChangedFile, yamlConfig *types.YAMLConfig, container *ServiceContainer) {
+	changedFiles []types.ChangedFile, yamlConfig *types.YAMLConfig, config *configs.Config, container *ServiceContainer) {
 
 	LogInfoCtx(ctx, "processing files with workflows", map[string]interface{}{
 		"file_count":     len(changedFiles),
@@ -353,6 +423,7 @@ func processFilesWithWorkflows(ctx context.Context, prNumber int, sourceCommitSH
 		container.FileStateService,
 		container.MetricsCollector,
 		container.MessageTemplater,
+		config,
 	)
 
 	// Process each workflow
diff --git a/services/webhook_handler_new_test.go b/services/webhook_handler_new_test.go
index d488ac3..2467d2f 100644
--- a/services/webhook_handler_new_test.go
+++ b/services/webhook_handler_new_test.go
@@ -2,6 +2,7 @@ package services
 
 import (
 	"bytes"
+	"context"
 	"crypto/hmac"
 	"crypto/rand"
 	"crypto/rsa"
@@ -13,11 +14,11 @@ import (
 	"encoding/pem"
 	"net/http"
 	"net/http/httptest"
-	"os"
 	"testing"
 
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/grove-platform/github-copier/configs"
+	"github.com/jarcoal/httpmock"
 )
 
 func TestSimpleVerifySignature(t *testing.T) {
@@ -83,6 +84,33 @@ func TestSimpleVerifySignature(t *testing.T) {
 	}
 }
 
+func TestHandleWebhookWithContainer_MethodNotAllowed(t *testing.T) {
+	config := &configs.Config{
+		ConfigRepoOwner: "test-owner",
+		ConfigRepoName:  "test-repo",
+		AuditEnabled:    false,
+	}
+
+	container, err := NewServiceContainer(config)
+	if err != nil {
+		t.Fatalf("NewServiceContainer() error = %v", err)
+	}
+
+	methods := []string{"GET", "PUT", "DELETE", "PATCH"}
+	for _, method := range methods {
+		t.Run(method, func(t *testing.T) {
+			req := httptest.NewRequest(method, "/events", nil)
+			w := httptest.NewRecorder()
+
+			HandleWebhookWithContainer(w, req, config, container)
+
+			if w.Code != http.StatusMethodNotAllowed {
+				t.Errorf("%s: status code = %d, want %d", method, w.Code, http.StatusMethodNotAllowed)
+			}
+		})
+	}
+}
+
 func TestHandleWebhookWithContainer_MissingEventType(t *testing.T) {
 	config := &configs.Config{
 		ConfigRepoOwner: "test-owner",
@@ -97,7 +125,7 @@ func TestHandleWebhookWithContainer_MissingEventType(t *testing.T) {
 	}
 
 	payload := []byte(`{"action": "closed"}`)
-	req := httptest.NewRequest("POST", "/webhook", bytes.NewReader(payload))
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
 	// Missing X-GitHub-Event header
 
 	w := httptest.NewRecorder()
@@ -128,7 +156,7 @@ func TestHandleWebhookWithContainer_InvalidSignature(t *testing.T) {
 	}
 
 	payload := []byte(`{"action": "closed"}`)
-	req := httptest.NewRequest("POST", "/webhook", bytes.NewReader(payload))
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
 	req.Header.Set("X-GitHub-Event", "pull_request")
 	req.Header.Set("X-Hub-Signature-256", "sha256=invalid")
 
@@ -158,10 +186,10 @@ func TestHandleWebhookWithContainer_ValidSignature(t *testing.T) {
 
 	// Create a valid pull_request event payload
 	prEvent := &github.PullRequestEvent{
-		Action: github.String("opened"),
+		Action: github.Ptr("opened"),
 		PullRequest: &github.PullRequest{
-			Number: github.Int(123),
-			Merged: github.Bool(false),
+			Number: github.Ptr(123),
+			Merged: github.Ptr(false),
 		},
 	}
 
@@ -172,7 +200,7 @@ func TestHandleWebhookWithContainer_ValidSignature(t *testing.T) {
 	mac.Write(payload)
 	signature := "sha256=" + hex.EncodeToString(mac.Sum(nil))
 
-	req := httptest.NewRequest("POST", "/webhook", bytes.NewReader(payload))
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
 	req.Header.Set("X-GitHub-Event", "pull_request")
 	req.Header.Set("X-Hub-Signature-256", signature)
 
@@ -205,7 +233,7 @@ func TestHandleWebhookWithContainer_NonPREvent(t *testing.T) {
 	}
 	payload, _ := json.Marshal(pushEvent)
 
-	req := httptest.NewRequest("POST", "/webhook", bytes.NewReader(payload))
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
 	req.Header.Set("X-GitHub-Event", "push")
 
 	w := httptest.NewRecorder()
@@ -233,15 +261,15 @@ func TestHandleWebhookWithContainer_NonMergedPR(t *testing.T) {
 
 	// Create a PR event that's not merged
 	prEvent := &github.PullRequestEvent{
-		Action: github.String("opened"),
+		Action: github.Ptr("opened"),
 		PullRequest: &github.PullRequest{
-			Number: github.Int(123),
-			Merged: github.Bool(false),
+			Number: github.Ptr(123),
+			Merged: github.Ptr(false),
 		},
 	}
 	payload, _ := json.Marshal(prEvent)
 
-	req := httptest.NewRequest("POST", "/webhook", bytes.NewReader(payload))
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
 	req.Header.Set("X-GitHub-Event", "pull_request")
 
 	w := httptest.NewRecorder()
@@ -261,26 +289,22 @@ func TestHandleWebhookWithContainer_MergedPR(t *testing.T) {
 	// the webhook handler returns the correct HTTP response.
 
 	// Set up environment variables to prevent ConfigurePermissions from failing
-	// We don't clean these up because:
-	// 1. The background goroutine may still need them after the test completes
-	// 2. TestMain in github_write_to_target_test.go sets them up properly anyway
-	// 3. These are test values that won't affect other tests
-	os.Setenv(configs.AppId, "123456")
-	os.Setenv(configs.InstallationId, "789012")
-	os.Setenv(configs.ConfigRepoOwner, "test-owner")
-	os.Setenv(configs.ConfigRepoName, "test-repo")
-	os.Setenv("SKIP_SECRET_MANAGER", "true")
+	// t.Setenv auto-cleans up after the test
+	t.Setenv(configs.AppId, "123456")
+	t.Setenv(configs.InstallationId, "789012")
+	t.Setenv(configs.ConfigRepoOwner, "test-owner")
+	t.Setenv(configs.ConfigRepoName, "test-repo")
+	t.Setenv("SKIP_SECRET_MANAGER", "true")
 
 	// Generate a valid RSA private key for testing
 	key, _ := rsa.GenerateKey(rand.Reader, 1024)
 	der := x509.MarshalPKCS1PrivateKey(key)
 	pemBytes := pem.EncodeToMemory(&pem.Block{Type: "RSA PRIVATE KEY", Bytes: der})
-	os.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
-	os.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
+	t.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
+	t.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
 
-	// Set InstallationAccessToken to prevent ConfigurePermissions from being called
-	// We don't reset this because the background goroutine may still need it after the test completes
-	InstallationAccessToken = "test-token"
+	// Set installation access token to prevent ConfigurePermissions from being called
+	defaultTokenManager.SetInstallationAccessToken("test-token")
 
 	config := &configs.Config{
 		ConfigRepoOwner: "test-owner",
@@ -296,31 +320,34 @@ func TestHandleWebhookWithContainer_MergedPR(t *testing.T) {
 
 	// Create a merged PR event
 	prEvent := &github.PullRequestEvent{
-		Action: github.String("closed"),
+		Action: github.Ptr("closed"),
 		PullRequest: &github.PullRequest{
-			Number:         github.Int(123),
-			Merged:         github.Bool(true),
-			MergeCommitSHA: github.String("abc123"),
+			Number:         github.Ptr(123),
+			Merged:         github.Ptr(true),
+			MergeCommitSHA: github.Ptr("abc123"),
 			Base: &github.PullRequestBranch{
-				Ref: github.String("main"),
+				Ref: github.Ptr("main"),
 			},
 		},
 		Repo: &github.Repository{
-			Name: github.String("test-repo"),
+			Name: github.Ptr("test-repo"),
 			Owner: &github.User{
-				Login: github.String("test-owner"),
+				Login: github.Ptr("test-owner"),
 			},
 		},
 	}
 	payload, _ := json.Marshal(prEvent)
 
-	req := httptest.NewRequest("POST", "/webhook", bytes.NewReader(payload))
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
 	req.Header.Set("X-GitHub-Event", "pull_request")
 
 	w := httptest.NewRecorder()
 
 	HandleWebhookWithContainer(w, req, config, container)
 
+	// Wait for background goroutine to finish to avoid race conditions during cleanup
+	container.Wait()
+
 	// Should return 202 Accepted for merged PRs
 	if w.Code != http.StatusAccepted {
 		t.Errorf("Status code = %d, want %d", w.Code, http.StatusAccepted)
@@ -332,9 +359,6 @@ func TestHandleWebhookWithContainer_MergedPR(t *testing.T) {
 	if response["status"] != "accepted" {
 		t.Errorf("Response status = %v, want accepted", response["status"])
 	}
-
-	// Note: The background goroutine will continue running and will eventually fail
-	// when trying to access GitHub APIs. This is expected and doesn't affect the test result.
 }
 
 func TestHandleWebhookWithContainer_MergedPRToDevelopmentBranch(t *testing.T) {
@@ -343,20 +367,20 @@ func TestHandleWebhookWithContainer_MergedPRToDevelopmentBranch(t *testing.T) {
 	// (assuming workflows are configured for main branch only)
 
 	// Set up environment variables
-	os.Setenv(configs.AppId, "123456")
-	os.Setenv(configs.InstallationId, "789012")
-	os.Setenv(configs.ConfigRepoOwner, "test-owner")
-	os.Setenv(configs.ConfigRepoName, "test-repo")
-	os.Setenv("SKIP_SECRET_MANAGER", "true")
+	t.Setenv(configs.AppId, "123456")
+	t.Setenv(configs.InstallationId, "789012")
+	t.Setenv(configs.ConfigRepoOwner, "test-owner")
+	t.Setenv(configs.ConfigRepoName, "test-repo")
+	t.Setenv("SKIP_SECRET_MANAGER", "true")
 
 	// Generate a valid RSA private key for testing
 	key, _ := rsa.GenerateKey(rand.Reader, 1024)
 	der := x509.MarshalPKCS1PrivateKey(key)
 	pemBytes := pem.EncodeToMemory(&pem.Block{Type: "RSA PRIVATE KEY", Bytes: der})
-	os.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
-	os.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
+	t.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
+	t.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
 
-	InstallationAccessToken = "test-token"
+	defaultTokenManager.SetInstallationAccessToken("test-token")
 
 	config := &configs.Config{
 		ConfigRepoOwner: "test-owner",
@@ -372,31 +396,34 @@ func TestHandleWebhookWithContainer_MergedPRToDevelopmentBranch(t *testing.T) {
 
 	// Create a merged PR event to development branch
 	prEvent := &github.PullRequestEvent{
-		Action: github.String("closed"),
+		Action: github.Ptr("closed"),
 		PullRequest: &github.PullRequest{
-			Number:         github.Int(456),
-			Merged:         github.Bool(true),
-			MergeCommitSHA: github.String("def456"),
+			Number:         github.Ptr(456),
+			Merged:         github.Ptr(true),
+			MergeCommitSHA: github.Ptr("def456"),
 			Base: &github.PullRequestBranch{
-				Ref: github.String("development"),
+				Ref: github.Ptr("development"),
 			},
 		},
 		Repo: &github.Repository{
-			Name: github.String("test-repo"),
+			Name: github.Ptr("test-repo"),
 			Owner: &github.User{
-				Login: github.String("test-owner"),
+				Login: github.Ptr("test-owner"),
 			},
 		},
 	}
 	payload, _ := json.Marshal(prEvent)
 
-	req := httptest.NewRequest("POST", "/webhook", bytes.NewReader(payload))
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
 	req.Header.Set("X-GitHub-Event", "pull_request")
 
 	w := httptest.NewRecorder()
 
 	HandleWebhookWithContainer(w, req, config, container)
 
+	// Wait for background goroutine to finish to avoid race conditions during cleanup
+	container.Wait()
+
 	// Should still return 202 Accepted (webhook accepts the event)
 	if w.Code != http.StatusAccepted {
 		t.Errorf("Status code = %d, want %d", w.Code, http.StatusAccepted)
@@ -408,11 +435,6 @@ func TestHandleWebhookWithContainer_MergedPRToDevelopmentBranch(t *testing.T) {
 	if response["status"] != "accepted" {
 		t.Errorf("Response status = %v, want accepted", response["status"])
 	}
-
-	// Note: The background goroutine will fail to find matching workflows
-	// because the workflow config specifies main branch, not development.
-	// This is the expected behavior - the webhook accepts the event but
-	// no workflows will be processed.
 }
 
 func TestHandleWebhookWithContainer_MergedPRWithDifferentBranches(t *testing.T) {
@@ -447,19 +469,19 @@ func TestHandleWebhookWithContainer_MergedPRWithDifferentBranches(t *testing.T)
 	}
 
 	// Set up environment variables
-	os.Setenv(configs.AppId, "123456")
-	os.Setenv(configs.InstallationId, "789012")
-	os.Setenv(configs.ConfigRepoOwner, "test-owner")
-	os.Setenv(configs.ConfigRepoName, "test-repo")
-	os.Setenv("SKIP_SECRET_MANAGER", "true")
+	t.Setenv(configs.AppId, "123456")
+	t.Setenv(configs.InstallationId, "789012")
+	t.Setenv(configs.ConfigRepoOwner, "test-owner")
+	t.Setenv(configs.ConfigRepoName, "test-repo")
+	t.Setenv("SKIP_SECRET_MANAGER", "true")
 
 	key, _ := rsa.GenerateKey(rand.Reader, 1024)
 	der := x509.MarshalPKCS1PrivateKey(key)
 	pemBytes := pem.EncodeToMemory(&pem.Block{Type: "RSA PRIVATE KEY", Bytes: der})
-	os.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
-	os.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
+	t.Setenv("GITHUB_APP_PRIVATE_KEY", string(pemBytes))
+	t.Setenv("GITHUB_APP_PRIVATE_KEY_B64", base64.StdEncoding.EncodeToString(pemBytes))
 
-	InstallationAccessToken = "test-token"
+	defaultTokenManager.SetInstallationAccessToken("test-token")
 
 	for _, tc := range testCases {
 		t.Run(tc.name, func(t *testing.T) {
@@ -477,31 +499,34 @@ func TestHandleWebhookWithContainer_MergedPRWithDifferentBranches(t *testing.T)
 
 			// Create a merged PR event with specific base branch
 			prEvent := &github.PullRequestEvent{
-				Action: github.String("closed"),
+				Action: github.Ptr("closed"),
 				PullRequest: &github.PullRequest{
-					Number:         github.Int(tc.prNumber),
-					Merged:         github.Bool(true),
-					MergeCommitSHA: github.String("abc123"),
+					Number:         github.Ptr(tc.prNumber),
+					Merged:         github.Ptr(true),
+					MergeCommitSHA: github.Ptr("abc123"),
 					Base: &github.PullRequestBranch{
-						Ref: github.String(tc.baseBranch),
+						Ref: github.Ptr(tc.baseBranch),
 					},
 				},
 				Repo: &github.Repository{
-					Name: github.String("test-repo"),
+					Name: github.Ptr("test-repo"),
 					Owner: &github.User{
-						Login: github.String("test-owner"),
+						Login: github.Ptr("test-owner"),
 					},
 				},
 			}
 			payload, _ := json.Marshal(prEvent)
 
-			req := httptest.NewRequest("POST", "/webhook", bytes.NewReader(payload))
+			req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
 			req.Header.Set("X-GitHub-Event", "pull_request")
 
 			w := httptest.NewRecorder()
 
 			HandleWebhookWithContainer(w, req, config, container)
 
+			// Wait for background goroutine to finish to avoid race conditions during cleanup
+			container.Wait()
+
 			// Should return 202 Accepted for all merged PRs
 			if w.Code != http.StatusAccepted {
 				t.Errorf("Status code = %d, want %d", w.Code, http.StatusAccepted)
@@ -517,16 +542,143 @@ func TestHandleWebhookWithContainer_MergedPRWithDifferentBranches(t *testing.T)
 	}
 }
 
+func TestHandleWebhookWithContainer_DuplicateDelivery(t *testing.T) {
+	config := &configs.Config{
+		ConfigRepoOwner: "test-owner",
+		ConfigRepoName:  "test-repo",
+		AuditEnabled:    false,
+	}
+
+	container, err := NewServiceContainer(config)
+	if err != nil {
+		t.Fatalf("NewServiceContainer() error = %v", err)
+	}
+
+	// Create a push event payload (non-PR, returns 204)
+	pushEvent := map[string]interface{}{
+		"ref": "refs/heads/main",
+	}
+	payload, _ := json.Marshal(pushEvent)
+
+	deliveryID := "test-delivery-abc-123"
+
+	// First request with this delivery ID should be processed normally
+	req1 := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
+	req1.Header.Set("X-GitHub-Event", "push")
+	req1.Header.Set("X-GitHub-Delivery", deliveryID)
+	w1 := httptest.NewRecorder()
+
+	HandleWebhookWithContainer(w1, req1, config, container)
+
+	if w1.Code != http.StatusNoContent {
+		t.Errorf("First request: status code = %d, want %d", w1.Code, http.StatusNoContent)
+	}
+
+	// Second request with the same delivery ID should be rejected as duplicate
+	req2 := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
+	req2.Header.Set("X-GitHub-Event", "push")
+	req2.Header.Set("X-GitHub-Delivery", deliveryID)
+	w2 := httptest.NewRecorder()
+
+	HandleWebhookWithContainer(w2, req2, config, container)
+
+	if w2.Code != http.StatusOK {
+		t.Errorf("Duplicate request: status code = %d, want %d (duplicate should return 200 OK)", w2.Code, http.StatusOK)
+	}
+
+	// Third request with a different delivery ID should be processed
+	req3 := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
+	req3.Header.Set("X-GitHub-Event", "push")
+	req3.Header.Set("X-GitHub-Delivery", "different-delivery-456")
+	w3 := httptest.NewRecorder()
+
+	HandleWebhookWithContainer(w3, req3, config, container)
+
+	if w3.Code != http.StatusNoContent {
+		t.Errorf("Different delivery: status code = %d, want %d", w3.Code, http.StatusNoContent)
+	}
+}
+
+func TestHandleWebhookWithContainer_NoDeliveryHeader(t *testing.T) {
+	config := &configs.Config{
+		ConfigRepoOwner: "test-owner",
+		ConfigRepoName:  "test-repo",
+		AuditEnabled:    false,
+	}
+
+	container, err := NewServiceContainer(config)
+	if err != nil {
+		t.Fatalf("NewServiceContainer() error = %v", err)
+	}
+
+	// Request without X-GitHub-Delivery header should still be processed
+	pushEvent := map[string]interface{}{
+		"ref": "refs/heads/main",
+	}
+	payload, _ := json.Marshal(pushEvent)
+
+	req := httptest.NewRequest("POST", "/events", bytes.NewReader(payload))
+	req.Header.Set("X-GitHub-Event", "push")
+	// No X-GitHub-Delivery header
+
+	w := httptest.NewRecorder()
+
+	HandleWebhookWithContainer(w, req, config, container)
+
+	if w.Code != http.StatusNoContent {
+		t.Errorf("Status code = %d, want %d", w.Code, http.StatusNoContent)
+	}
+}
+
 func TestRetrieveFileContentsWithConfigAndBranch(t *testing.T) {
-	// This test would require mocking the GitHub client
-	// For now, we document the expected behavior
-	t.Skip("Skipping test that requires GitHub API mocking")
-
-	// Expected behavior:
-	// - Should call client.Repositories.GetContents with correct parameters
-	// - Should use the specified branch in RepositoryContentGetOptions
-	// - Should return file content on success
-	// - Should return error on failure
+	// Use global httpmock since the REST client constructed inside the function
+	// creates its own http.Client transport chain.
+	httpmock.Activate()
+	t.Cleanup(httpmock.DeactivateAndReset)
+
+	owner := "test-owner"
+	repo := "test-repo"
+	branch := "main"
+	filePath := "examples/hello.go"
+	expectedContent := "package main\n\nfunc main() {}\n"
+
+	defaultTokenManager.SetInstallationAccessToken("test-token")
+	SetInstallationTokenForOrg(owner, "test-token")
+
+	httpmock.RegisterResponder("GET",
+		"https://api.github.com/repos/"+owner+"/"+repo+"/contents/"+filePath,
+		httpmock.NewJsonResponderOrPanic(200, map[string]any{
+			"type":     "file",
+			"name":     "hello.go",
+			"path":     filePath,
+			"encoding": "base64",
+			"content":  base64.StdEncoding.EncodeToString([]byte(expectedContent)),
+		}),
+	)
+
+	config := &configs.Config{
+		ConfigRepoOwner: owner,
+		ConfigRepoName:  repo,
+	}
+
+	fileContent, err := RetrieveFileContentsWithConfigAndBranch(
+		context.Background(), config, filePath, branch, owner, repo,
+	)
+	if err != nil {
+		t.Fatalf("RetrieveFileContentsWithConfigAndBranch: %v", err)
+	}
+
+	if fileContent == nil {
+		t.Fatal("expected non-nil file content")
+	}
+
+	content, err := fileContent.GetContent()
+	if err != nil {
+		t.Fatalf("GetContent: %v", err)
+	}
+	if content != expectedContent {
+		t.Errorf("content = %q, want %q", content, expectedContent)
+	}
 }
 
 func TestMaxWebhookBodyBytes(t *testing.T) {
diff --git a/services/workflow_processor.go b/services/workflow_processor.go
index a766907..169cdd8 100644
--- a/services/workflow_processor.go
+++ b/services/workflow_processor.go
@@ -8,13 +8,14 @@ import (
 	"time"
 
 	"github.com/bmatcuk/doublestar/v4"
-	"github.com/google/go-github/v48/github"
-	. "github.com/grove-platform/github-copier/types"
+	"github.com/google/go-github/v82/github"
+	"github.com/grove-platform/github-copier/configs"
+	"github.com/grove-platform/github-copier/types"
 )
 
 // WorkflowProcessor processes workflows and applies transformations
 type WorkflowProcessor interface {
-	ProcessWorkflow(ctx context.Context, workflow Workflow, changedFiles []ChangedFile, prNumber int, sourceCommitSHA string) error
+	ProcessWorkflow(ctx context.Context, workflow types.Workflow, changedFiles []types.ChangedFile, prNumber int, sourceCommitSHA string) error
 }
 
 // workflowProcessor implements WorkflowProcessor
@@ -24,6 +25,7 @@ type workflowProcessor struct {
 	fileStateService FileStateService
 	metricsCollector *MetricsCollector
 	messageTemplater MessageTemplater
+	config           *configs.Config
 }
 
 // NewWorkflowProcessor creates a new workflow processor
@@ -33,6 +35,7 @@ func NewWorkflowProcessor(
 	fileStateService FileStateService,
 	metricsCollector *MetricsCollector,
 	messageTemplater MessageTemplater,
+	config *configs.Config,
 ) WorkflowProcessor {
 	return &workflowProcessor{
 		patternMatcher:   patternMatcher,
@@ -40,14 +43,15 @@ func NewWorkflowProcessor(
 		fileStateService: fileStateService,
 		metricsCollector: metricsCollector,
 		messageTemplater: messageTemplater,
+		config:           config,
 	}
 }
 
 // ProcessWorkflow processes a single workflow
 func (wp *workflowProcessor) ProcessWorkflow(
 	ctx context.Context,
-	workflow Workflow,
-	changedFiles []ChangedFile,
+	workflow types.Workflow,
+	changedFiles []types.ChangedFile,
 	prNumber int,
 	sourceCommitSHA string,
 ) error {
@@ -92,8 +96,8 @@ func (wp *workflowProcessor) ProcessWorkflow(
 // processFileForWorkflow processes a single file for a workflow
 func (wp *workflowProcessor) processFileForWorkflow(
 	ctx context.Context,
-	workflow Workflow,
-	file ChangedFile,
+	workflow types.Workflow,
+	file types.ChangedFile,
 	prNumber int,
 	sourceCommitSHA string,
 ) (bool, error) {
@@ -154,18 +158,18 @@ func (wp *workflowProcessor) processFileForWorkflow(
 // applyTransformation applies a transformation to a file path
 func (wp *workflowProcessor) applyTransformation(
 	ctx context.Context,
-	workflow Workflow,
-	transformation Transformation,
+	workflow types.Workflow,
+	transformation types.Transformation,
 	sourcePath string,
 ) (matched bool, targetPath string, err error) {
 	switch transformation.GetType() {
-	case TransformationTypeMove:
+	case types.TransformationTypeMove:
 		return wp.applyMoveTransformation(transformation.Move, sourcePath)
-	case TransformationTypeCopy:
+	case types.TransformationTypeCopy:
 		return wp.applyCopyTransformation(transformation.Copy, sourcePath)
-	case TransformationTypeGlob:
+	case types.TransformationTypeGlob:
 		return wp.applyGlobTransformation(transformation.Glob, sourcePath)
-	case TransformationTypeRegex:
+	case types.TransformationTypeRegex:
 		return wp.applyRegexTransformation(transformation.Regex, sourcePath)
 	default:
 		return false, "", fmt.Errorf("unknown transformation type: %s", transformation.GetType())
@@ -174,7 +178,7 @@ func (wp *workflowProcessor) applyTransformation(
 
 // applyMoveTransformation applies a move transformation
 func (wp *workflowProcessor) applyMoveTransformation(
-	move *MoveTransform,
+	move *types.MoveTransform,
 	sourcePath string,
 ) (matched bool, targetPath string, err error) {
 	// Check if source path starts with the "from" prefix
@@ -197,7 +201,7 @@ func (wp *workflowProcessor) applyMoveTransformation(
 
 // applyCopyTransformation applies a copy transformation
 func (wp *workflowProcessor) applyCopyTransformation(
-	copy *CopyTransform,
+	copy *types.CopyTransform,
 	sourcePath string,
 ) (matched bool, targetPath string, err error) {
 	// Copy only matches exact file path
@@ -209,7 +213,7 @@ func (wp *workflowProcessor) applyCopyTransformation(
 
 // applyGlobTransformation applies a glob transformation
 func (wp *workflowProcessor) applyGlobTransformation(
-	glob *GlobTransform,
+	glob *types.GlobTransform,
 	sourcePath string,
 ) (matched bool, targetPath string, err error) {
 	// Use doublestar for glob matching
@@ -235,12 +239,12 @@ func (wp *workflowProcessor) applyGlobTransformation(
 
 // applyRegexTransformation applies a regex transformation
 func (wp *workflowProcessor) applyRegexTransformation(
-	regex *RegexTransform,
+	regex *types.RegexTransform,
 	sourcePath string,
 ) (matched bool, targetPath string, err error) {
 	// Use existing pattern matcher for regex
-	sourcePattern := SourcePattern{
-		Type:    PatternTypeRegex,
+	sourcePattern := types.SourcePattern{
+		Type:    types.PatternTypeRegex,
 		Pattern: regex.Pattern,
 	}
 
@@ -285,7 +289,7 @@ func (wp *workflowProcessor) isExcluded(path string, excludePatterns []string) b
 	for _, pattern := range excludePatterns {
 		matched, err := doublestar.Match(pattern, path)
 		if err != nil {
-			LogWarning(fmt.Sprintf("Invalid exclude pattern: %s: %v", pattern, err))
+			LogWarning("Invalid exclude pattern", "pattern", pattern, "error", err)
 			continue
 		}
 		if matched {
@@ -296,13 +300,13 @@ func (wp *workflowProcessor) isExcluded(path string, excludePatterns []string) b
 }
 
 // addToDeprecationMap adds a file to the deprecation map
-func (wp *workflowProcessor) addToDeprecationMap(workflow Workflow, targetPath string) {
+func (wp *workflowProcessor) addToDeprecationMap(workflow types.Workflow, targetPath string) {
 	deprecationFile := "deprecated_examples.json"
 	if workflow.DeprecationCheck != nil && workflow.DeprecationCheck.File != "" {
 		deprecationFile = workflow.DeprecationCheck.File
 	}
 
-	entry := DeprecatedFileEntry{
+	entry := types.DeprecatedFileEntry{
 		FileName: targetPath,
 		Repo:     workflow.Destination.Repo,
 		Branch:   workflow.Destination.Branch,
@@ -314,8 +318,8 @@ func (wp *workflowProcessor) addToDeprecationMap(workflow Workflow, targetPath s
 // addToUploadQueue adds a file to the upload queue
 func (wp *workflowProcessor) addToUploadQueue(
 	ctx context.Context,
-	workflow Workflow,
-	file ChangedFile,
+	workflow types.Workflow,
+	file types.ChangedFile,
 	targetPath string,
 	prNumber int,
 	sourceCommitSHA string,
@@ -329,16 +333,16 @@ func (wp *workflowProcessor) addToUploadQueue(
 	sourceRepoName := parts[1]
 
 	// Fetch file content from source repository
-	fileContent, err := RetrieveFileContentsWithConfigAndBranch(ctx, file.Path, sourceCommitSHA, sourceRepoOwner, sourceRepoName)
+	fileContent, err := RetrieveFileContentsWithConfigAndBranch(ctx, wp.config, file.Path, sourceCommitSHA, sourceRepoOwner, sourceRepoName)
 	if err != nil {
 		return fmt.Errorf("failed to retrieve file content: %w", err)
 	}
 
 	// Update file name to target path
-	fileContent.Name = github.String(targetPath)
+	fileContent.Name = github.Ptr(targetPath)
 
 	// Create upload key
-	key := UploadKey{
+	key := types.UploadKey{
 		RepoName:   workflow.Destination.Repo,
 		BranchPath: workflow.Destination.Branch,
 	}
@@ -347,9 +351,9 @@ func (wp *workflowProcessor) addToUploadQueue(
 	filesToUpload := wp.fileStateService.GetFilesToUpload()
 	content, exists := filesToUpload[key]
 	if !exists {
-		content = UploadFileContent{
+		content = types.UploadFileContent{
 			Content:        []github.RepositoryContent{},
-			CommitStrategy: CommitStrategy(getCommitStrategyType(workflow)),
+			CommitStrategy: types.CommitStrategy(getCommitStrategyType(workflow)),
 			UsePRTemplate:  getUsePRTemplate(workflow),
 			AutoMergePR:    getAutoMerge(workflow),
 		}
@@ -359,7 +363,7 @@ func (wp *workflowProcessor) addToUploadQueue(
 	content.Content = append(content.Content, *fileContent)
 
 	// Render templates with message context
-	msgCtx := NewMessageContext()
+	msgCtx := types.NewMessageContext()
 	msgCtx.SourceRepo = workflow.Source.Repo
 	msgCtx.SourceBranch = workflow.Source.Branch
 	msgCtx.TargetRepo = workflow.Destination.Repo
@@ -400,21 +404,21 @@ func (wp *workflowProcessor) addToUploadQueue(
 
 // Helper functions to extract config values
 
-func getCommitStrategyType(workflow Workflow) string {
+func getCommitStrategyType(workflow types.Workflow) string {
 	if workflow.CommitStrategy != nil && workflow.CommitStrategy.Type != "" {
 		return workflow.CommitStrategy.Type
 	}
 	return "pull_request" // default
 }
 
-func getUsePRTemplate(workflow Workflow) bool {
+func getUsePRTemplate(workflow types.Workflow) bool {
 	if workflow.CommitStrategy != nil {
 		return workflow.CommitStrategy.UsePRTemplate
 	}
 	return false
 }
 
-func getAutoMerge(workflow Workflow) bool {
+func getAutoMerge(workflow types.Workflow) bool {
 	if workflow.CommitStrategy != nil {
 		return workflow.CommitStrategy.AutoMerge
 	}
diff --git a/services/workflow_processor_test.go b/services/workflow_processor_test.go
index 6ea30db..233fe7f 100644
--- a/services/workflow_processor_test.go
+++ b/services/workflow_processor_test.go
@@ -8,6 +8,8 @@ import (
 	"github.com/grove-platform/github-copier/types"
 	"github.com/stretchr/testify/assert"
 	"github.com/stretchr/testify/require"
+
+	test "github.com/grove-platform/github-copier/tests"
 )
 
 // ============================================================================
@@ -154,6 +156,7 @@ func TestWorkflowProcessor_MoveTransformation(t *testing.T) {
 				fileStateService,
 				nil, // metrics collector
 				&mockMessageTemplater{},
+				test.TestConfig(),
 			)
 
 			workflow := createTestWorkflow("test-workflow", []types.Transformation{
@@ -223,6 +226,7 @@ func TestWorkflowProcessor_CopyTransformation(t *testing.T) {
 				fileStateService,
 				nil,
 				&mockMessageTemplater{},
+				test.TestConfig(),
 			)
 
 			workflow := createTestWorkflow("test-workflow", []types.Transformation{
@@ -297,6 +301,7 @@ func TestWorkflowProcessor_GlobTransformation(t *testing.T) {
 				fileStateService,
 				nil,
 				&mockMessageTemplater{},
+				test.TestConfig(),
 			)
 
 			workflow := createTestWorkflow("test-workflow", []types.Transformation{
@@ -364,6 +369,7 @@ func TestWorkflowProcessor_RegexTransformation(t *testing.T) {
 				fileStateService,
 				nil,
 				&mockMessageTemplater{},
+				test.TestConfig(),
 			)
 
 			workflow := createTestWorkflow("test-workflow", []types.Transformation{
@@ -452,6 +458,7 @@ func TestWorkflowProcessor_ExcludePatterns(t *testing.T) {
 				fileStateService,
 				nil,
 				&mockMessageTemplater{},
+				test.TestConfig(),
 			)
 
 			workflow := types.Workflow{
@@ -503,6 +510,7 @@ func TestWorkflowProcessor_MultipleTransformations(t *testing.T) {
 		fileStateService,
 		nil,
 		&mockMessageTemplater{},
+		test.TestConfig(),
 	)
 
 	workflow := types.Workflow{
@@ -564,6 +572,7 @@ func TestWorkflowProcessor_EmptyChangedFiles(t *testing.T) {
 		fileStateService,
 		nil,
 		&mockMessageTemplater{},
+		test.TestConfig(),
 	)
 
 	workflow := createTestWorkflow("test-workflow", []types.Transformation{
@@ -587,6 +596,7 @@ func TestWorkflowProcessor_NoTransformations(t *testing.T) {
 		fileStateService,
 		nil,
 		&mockMessageTemplater{},
+		test.TestConfig(),
 	)
 
 	workflow := createTestWorkflow("test-workflow", []types.Transformation{})
@@ -614,6 +624,7 @@ func TestWorkflowProcessor_InvalidExcludePattern(t *testing.T) {
 		fileStateService,
 		nil,
 		&mockMessageTemplater{},
+		test.TestConfig(),
 	)
 
 	workflow := types.Workflow{
@@ -658,6 +669,7 @@ func TestWorkflowProcessor_CustomDeprecationFile(t *testing.T) {
 		fileStateService,
 		nil,
 		&mockMessageTemplater{},
+		test.TestConfig(),
 	)
 
 	workflow := types.Workflow{
@@ -733,6 +745,7 @@ func TestWorkflowProcessor_FileStatusHandling(t *testing.T) {
 				fileStateService,
 				nil,
 				&mockMessageTemplater{},
+				test.TestConfig(),
 			)
 
 			workflow := createTestWorkflow("test-workflow", []types.Transformation{
@@ -811,6 +824,7 @@ func TestWorkflowProcessor_PathTransformationEdgeCases(t *testing.T) {
 				fileStateService,
 				nil,
 				&mockMessageTemplater{},
+				test.TestConfig(),
 			)
 
 			workflow := createTestWorkflow("test-workflow", []types.Transformation{tt.transform})
diff --git a/testdata/README.md b/testdata/README.md
index 8497088..ab93b50 100644
--- a/testdata/README.md
+++ b/testdata/README.md
@@ -16,7 +16,7 @@ cp testdata/.env.test .env.test
 ENV_FILE=.env.test go run app.go
 
 # 4. In another terminal, start webhook tunnel
-smee --url https://smee.io/YOUR_CHANNEL --target http://localhost:8080/webhook
+smee --url https://smee.io/YOUR_CHANNEL --target http://localhost:8080/events
 
 # 5. Create a PR in your test source repo and merge it
 ```
@@ -189,10 +189,10 @@ After sending a test webhook:
 1. **Check Application Logs**
    ```bash
    # Local
-   tail -f logs/app.log
+   # Logs go to stdout (JSON format via slog)
    
-   # GCP
-   gcloud app logs tail -s default
+   # Cloud Run
+   gcloud run services logs read github-copier --limit=50
    ```
 
 2. **Check Metrics**
diff --git a/tests/utils.go b/tests/utils.go
index 4bc2ff2..401effa 100644
--- a/tests/utils.go
+++ b/tests/utils.go
@@ -30,20 +30,38 @@ func EnvOwnerRepo(t testing.TB) (string, string) {
 	return owner, repo
 }
 
+// TestConfig returns a *configs.Config populated from the current environment variables.
+// This mirrors the values set in TestMain for test suites.
+func TestConfig() *configs.Config {
+	cfg := configs.NewConfig()
+	cfg.ConfigRepoOwner = os.Getenv(configs.ConfigRepoOwner)
+	cfg.ConfigRepoName = os.Getenv(configs.ConfigRepoName)
+	cfg.InstallationId = os.Getenv(configs.InstallationId)
+	cfg.AppId = os.Getenv(configs.AppId)
+	cfg.AppClientId = os.Getenv(configs.AppClientId)
+	cfg.ConfigRepoBranch = os.Getenv(configs.ConfigRepoBranch)
+	if cfg.ConfigRepoBranch == "" {
+		cfg.ConfigRepoBranch = "main"
+	}
+	return cfg
+}
+
 //
 // HTTP/test wiring helpers
 //
 
-// WithHTTPMock wraps a test in `httpmock` activation on a dedicated http.Client and routes services.HTTPClient through it.
-// Used in any test that needs multiple mock endpoints. Wrap t.Run blocks to avoid leftover mocks affecting other tests.
+// WithHTTPMock wraps a test in `httpmock` activation on a dedicated http.Client
+// and routes the TokenManager's HTTP client through it.
 func WithHTTPMock(t testing.TB) *http.Client {
 	t.Helper()
 	c := &http.Client{}
 	httpmock.ActivateNonDefault(c)
 	t.Cleanup(func() { httpmock.DeactivateAndReset() })
-	prev := services.HTTPClient
-	services.HTTPClient = c
-	t.Cleanup(func() { services.HTTPClient = prev })
+
+	tm := services.DefaultTokenManager()
+	prev := tm.GetHTTPClient()
+	tm.SetHTTPClient(c)
+	t.Cleanup(func() { tm.SetHTTPClient(prev) })
 	return c
 }
 
@@ -60,7 +78,6 @@ func DumpHttpmockCalls(t testing.TB) {
 //
 
 // MockGitHubAppTokenEndpoint mocks the GitHub App installation token endpoint with a fixed fake token.
-// Used in to simulate any auth-triggered flow without needing a real installation ID.
 func MockGitHubAppTokenEndpoint(installationID string) {
 	httpmock.RegisterResponder("POST",
 		"https://api.github.com/app/installations/"+installationID+"/access_tokens",
@@ -69,7 +86,6 @@ func MockGitHubAppTokenEndpoint(installationID string) {
 }
 
 // MockGitHubAppInstallations mocks the GitHub App installations list endpoint.
-// Used to simulate fetching installation IDs for organizations.
 func MockGitHubAppInstallations(orgToInstallationID map[string]string) {
 	installations := []map[string]any{}
 	for org, installID := range orgToInstallationID {
@@ -93,8 +109,7 @@ func SetupOrgToken(org, token string) {
 	services.SetInstallationTokenForOrg(org, token)
 }
 
-// MockGitHubWriteEndpoints mocks the full direct-commit flow endpoints for a single branch: GET base ref, POST trees, POST commits, PATCH ref.
-// Used to simulate writing to a GitHub repo without creating a PR.
+// MockGitHubWriteEndpoints mocks the full direct-commit flow endpoints for a single branch.
 // Returns the URLs for the base ref, commits, and update ref endpoints.
 func MockGitHubWriteEndpoints(owner, repo, branch string) (baseRefURL, commitsURL, updateRefURL string) {
 	baseRefURL = "https://api.github.com/repos/" + owner + "/" + repo + "/git/ref/heads/" + branch
@@ -131,7 +146,6 @@ func MockGitHubWriteEndpoints(owner, repo, branch string) (baseRefURL, commitsUR
 }
 
 // MockContentsEndpoint mocks GET file contents for a given path/ref.
-// Used to simulate reading a file from a GitHub repo.
 func MockContentsEndpoint(owner, repo, path, contentB64 string) {
 	re := regexp.MustCompile(
 		`^https://api\.github\.com/repos/` + regexp.QuoteMeta(owner) + `/` +
@@ -149,7 +163,6 @@ func MockContentsEndpoint(owner, repo, path, contentB64 string) {
 }
 
 // MockCreateRef mocks POST to create a new temp branch ref. Returns the exact URL for call-count asserts.
-// Used to simulate creating a new branch for writing files without actually pushing to GitHub.
 func MockCreateRef(owner, repo string) string {
 	url := "https://api.github.com/repos/" + owner + "/" + repo + "/git/refs"
 	httpmock.RegisterResponder("POST", url,
@@ -162,7 +175,6 @@ func MockCreateRef(owner, repo string) string {
 }
 
 // MockPullsAndMerge mocks creating and merging a PR.
-// Used to simulate the full PR flow for functions that create a PR and then merge it
 func MockPullsAndMerge(owner, repo string, number int) {
 	httpmock.RegisterResponder("POST",
 		"https://api.github.com/repos/"+owner+"/"+repo+"/pulls",
@@ -175,7 +187,6 @@ func MockPullsAndMerge(owner, repo string, number int) {
 }
 
 // MockDeleteTempRef mocks DELETE to remove a temporary branch ref.
-// Used to simulate cleaning up after writing files without actually deleting a branch on GitHub.
 func MockDeleteTempRef(owner, repo string) {
 	re := regexp.MustCompile(
 		`^https://api\.github\.com/repos/` + regexp.QuoteMeta(owner) + `/` +
@@ -188,7 +199,7 @@ func MockDeleteTempRef(owner, repo string) {
 // Staging/assertion helpers
 //
 
-// NormalizeUpload flattens FilesToUpload to UploadKey -> []names for simpler comparisons.
+// NormalizeUpload flattens a FilesToUpload map to UploadKey -> []names for simpler comparisons.
 func NormalizeUpload(in map[types.UploadKey]types.UploadFileContent) map[types.UploadKey][]string {
 	out := make(map[types.UploadKey][]string, len(in))
 	for k, v := range in {
@@ -206,103 +217,12 @@ func MakeChanged(status, path string) types.ChangedFile {
 	return types.ChangedFile{Status: status, Path: path}
 }
 
-// ResetGlobals clears FilesToUpload and FilesToDeprecate.
-func ResetGlobals() {
-	services.FilesToUpload = nil
-	services.FilesToDeprecate = nil
-}
-
-// AssertUploadedPaths asserts that the staged filenames match the want for the given repo/branch (order-insensitive).
-func AssertUploadedPaths(t *testing.T, repo, branch string, want []string) {
-	t.Helper()
-	key := types.UploadKey{RepoName: repo, BranchPath: "refs/heads/" + branch}
-	got, ok := services.FilesToUpload[key]
-	if !ok {
-		t.Fatalf("expected FilesToUpload to contain key for %s/%s", repo, branch)
-	}
-
-	var names []string
-	for _, c := range got.Content {
-		n := c.GetName()
-		if n == "" {
-			n = c.GetPath() // fallback: some code paths populate only Path
-		}
-		names = append(names, n)
-	}
-
-	// exact, order-insensitive comparison
-	if len(want) == 0 && len(names) == 0 {
-		return
-	}
-	if len(want) != len(names) {
-		t.Fatalf("staged names length mismatch: got=%v want=%v", names, want)
-	}
-	wantSet := map[string]struct{}{}
-	for _, w := range want {
-		wantSet[w] = struct{}{}
-	}
-	for _, n := range names {
-		if _, ok := wantSet[n]; !ok {
-			t.Fatalf("unexpected staged path %q; got=%v want=%v", n, names, want)
-		}
-	}
-}
-
-// AssertUploadedPathsFromConfig converts staged source paths to target paths using cfg,
-// then compares against want - i.e. target paths (order-insensitive).
-// Used when the staged files are from a config that specifies source/target directories.
-func AssertUploadedPathsFromConfig(t *testing.T, cfg types.Configs, want []string) {
-	t.Helper()
-	key := types.UploadKey{RepoName: cfg.TargetRepo, BranchPath: "refs/heads/" + cfg.TargetBranch}
-	got, ok := services.FilesToUpload[key]
-	if !ok {
-		t.Fatalf("expected FilesToUpload to contain key for %s/%s", cfg.TargetRepo, cfg.TargetBranch)
-	}
-	var names []string
-	for _, c := range got.Content {
-		// Prefer Name if present
-		n := c.GetName()
-		if n == "" {
-			n = c.GetPath() // usually the *source* path (e.g. examples/…)
-		}
-		// If the staged name looks like a source path, rewrite to target
-		if cfg.SourceDirectory != "" && strings.HasPrefix(n, cfg.SourceDirectory) {
-			rel := strings.TrimPrefix(n, cfg.SourceDirectory)
-			rel = strings.TrimPrefix(rel, "/")
-			n = cfg.TargetDirectory
-			if rel != "" {
-				n = cfg.TargetDirectory + "/" + rel
-			}
-		}
-		names = append(names, n)
-	}
-
-	// order-insensitive compare
-	if len(want) == 0 && len(names) == 0 {
-		return
-	}
-	if len(want) != len(names) {
-		t.Fatalf("staged names length mismatch: got=%v want=%v", names, want)
-	}
-	wantSet := map[string]struct{}{}
-	for _, w := range want {
-		wantSet[w] = struct{}{}
-	}
-	for _, n := range names {
-		if _, ok = wantSet[n]; !ok {
-			t.Fatalf("unexpected staged path %q; got=%v want=%v", n, names, want)
-		}
-	}
-}
-
 // CountByMethodAndURLRegexp adds up call counts for a given METHOD whose stored httpmock key's URL matches urlRE.
-// Works for both exact and regex-registered responders.
-// Used to assert that a specific endpoint was called a certain number of times.
 func CountByMethodAndURLRegexp(method string, urlRE *regexp.Regexp) int {
 	info := httpmock.GetCallCountInfo()
 	total := 0
 	for k, v := range info {
-		if !(strings.HasPrefix(k, method+" ") || strings.HasPrefix(k, method+"=~")) {
+		if !strings.HasPrefix(k, method+" ") && !strings.HasPrefix(k, method+"=~") {
 			continue
 		}
 		var urlish string
@@ -324,7 +244,7 @@ func CountByMethodAndURLRegexp(method string, urlRE *regexp.Regexp) int {
 }
 
 // GetRefGetCount counts GET calls to /git/ref/(refs/)?heads/<branch>
-// for the given owner/repo/branch. Used to assert that a ref was fetched.
+// for the given owner/repo/branch.
 func GetRefGetCount(owner, repo, branch string) int {
 	re := regexp.MustCompile(`/repos/` + regexp.QuoteMeta(owner) + `/` + regexp.QuoteMeta(repo) +
 		`/git/ref/(?:refs/)?heads/` + regexp.QuoteMeta(branch) + `$`)
diff --git a/types/types.go b/types/types.go
index 9cb346f..2892b4d 100644
--- a/types/types.go
+++ b/types/types.go
@@ -1,7 +1,7 @@
 package types
 
 import (
-	"github.com/google/go-github/v48/github"
+	"github.com/google/go-github/v82/github"
 	"github.com/shurcooL/githubv4"
 )
 
@@ -103,8 +103,8 @@ type DeprecatedFileEntry struct {
 type UploadKey struct {
 	RepoName       string `json:"repo_name"`
 	BranchPath     string `json:"branch_path"`
-	RuleName       string `json:"rule_name"`        // Include rule name to allow multiple rules targeting same repo/branch
-	CommitStrategy string `json:"commit_strategy"`  // Include strategy to differentiate direct vs PR
+	RuleName       string `json:"rule_name"`       // Include rule name to allow multiple rules targeting same repo/branch
+	CommitStrategy string `json:"commit_strategy"` // Include strategy to differentiate direct vs PR
 }
 
 type UploadFileContent struct {
@@ -114,7 +114,7 @@ type UploadFileContent struct {
 	CommitMessage  string                     `json:"commit_message,omitempty"`
 	PRTitle        string                     `json:"pr_title,omitempty"`
 	PRBody         string                     `json:"pr_body,omitempty"`
-	UsePRTemplate  bool                       `json:"use_pr_template,omitempty"`  // If true, fetch and merge PR template from target repo
+	UsePRTemplate  bool                       `json:"use_pr_template,omitempty"` // If true, fetch and merge PR template from target repo
 	AutoMergePR    bool                       `json:"auto_merge_pr,omitempty"`
 }