docs: mark Phase 2 persistence mission complete

.gitignore

@@ -21,3 +21,4 @@ Thumbs.db
 # Logs
 *.log
 .gitnexus
+Cargo.lock

AGENTS.md

@@ -1,7 +1,7 @@
 <!-- gitnexus:start -->
 # GitNexus MCP
 
-This project is indexed by GitNexus as **cipherocto** (120 symbols, 140 relationships, 2 execution flows).
+This project is indexed by GitNexus as **cipherocto** (227 symbols, 328 relationships, 10 execution flows).
 
 GitNexus provides a knowledge graph over this codebase — call chains, blast radius, execution flows, and semantic search.
 
@@ -59,4 +59,4 @@ MATCH (caller)-[:CodeRelation {type: 'CALLS'}]->(f:Function {name: "myFunc"})
 RETURN caller.name, caller.filePath
 ```
 
-<!-- gitnexus:end -->
+<!-- gitnexus:end -->

CLAUDE.md

@@ -77,7 +77,17 @@ Every participant stakes both OCTO (global alignment) + Role Token (local specia
 
 ## Development Workflow
 
-Since this is documentation-only, there are no build, test, or lint commands.
+### Rust Development Commands
+
+**Lint (must pass with zero warnings)**
+```bash
+cargo clippy --all-targets --all-features -- -D warnings
+```
+
+**Format**
+```bash
+cargo fmt
+```
 
 ### Documentation Script
 
@@ -111,10 +121,36 @@ CipherOcto uses **Trunk-Based + Feature Streams**:
 Full documentation: `.github/BRANCH_STRATEGY.md`
 Branch protection rules: `.github/branch-protection-rules.md`
 
+## Documentation Standards
+
+**Diagrams:** Always prefer Mermaid diagrams over ASCII art. Mermaid is:
+- Rendered in GitHub, VS Code, and most Markdown viewers
+- Easier to maintain and edit
+- Consistent with modern documentation practices
+
+**Example:**
+```mermaid
+graph TD
+    A[Start] --> B{Decision}
+    B -->|Yes| C[Action 1]
+    B -->|No| D[Action 2]
+```
+
+**When creating or updating docs:**
+- Use `mermaid` code blocks for flowcharts, state diagrams, sequence diagrams
+- Avoid ASCII art (`┌─`, `└─`, `─►`, etc.)
+- If existing ASCII diagrams exist, convert them to Mermaid
+
+**Markdown Formatting:**
+- All markdown files must pass Prettier formatting
+- Run `npx prettier --write <file>.md` before committing
+- Ensure files end with a newline
+- Use consistent heading hierarchy (no skipping levels)
+
 <!-- gitnexus:start -->
 # GitNexus MCP
 
-This project is indexed by GitNexus as **cipherocto** (60 files, 120 symbols, 2 execution flows).
+This project is indexed by GitNexus as **cipherocto** (227 symbols, 328 relationships, 10 execution flows).
 
 GitNexus provides a knowledge graph over this codebase — call chains, blast radius, execution flows, and semantic search.
 
@@ -149,15 +185,6 @@ For any task involving code understanding, debugging, impact analysis, or refact
 | `cypher` | Raw graph queries (read `gitnexus://repo/{name}/schema` first) |
 | `list_repos` | Discover indexed repos |
 
-## Current Codebase Structure
-
-**Functional Areas (Clusters):**
-- Cluster_1: 5 symbols, 89% cohesion
-
-**Execution Flows (Processes):**
-- Main → Open_db: 4 steps (cross-community)
-- Main → Execute_agent: 3 steps (intra-community)
-
 ## Resources Reference
 
 Lightweight reads (~100-500 tokens) for navigation: