From 3b927f4e3a52127d85912da2908c1cc484dd9779 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Tue, 24 Feb 2026 19:42:56 +0000
Subject: [PATCH 01/10] cortex config

---
 src/vscode-docker/.devcontainer.json      |  2 +-
 src/vscode-docker/create-cortex-config.sh | 90 +++++++++++++++++++++++
 2 files changed, 91 insertions(+), 1 deletion(-)
 create mode 100644 src/vscode-docker/create-cortex-config.sh

diff --git a/src/vscode-docker/.devcontainer.json b/src/vscode-docker/.devcontainer.json
index 7a57f43c..b47feed3 100644
--- a/src/vscode-docker/.devcontainer.json
+++ b/src/vscode-docker/.devcontainer.json
@@ -5,7 +5,7 @@
   "shutdownAction": "none",
   "workspaceFolder": "/workspace",
   "postCreateCommand":
-    "./startupscript/post-startup.sh abc /config \"${templateOption:cloud}\" \"${templateOption:login}\"",
+    "./startupscript/post-startup.sh abc /config \"${templateOption:cloud}\" \"${templateOption:login}\"; bash ./create-cortex-config.sh /config",
   // re-mount bucket files on container start up
   "postStartCommand": [
     "./startupscript/remount-on-restart.sh",
diff --git a/src/vscode-docker/create-cortex-config.sh b/src/vscode-docker/create-cortex-config.sh
new file mode 100644
index 00000000..0c61dd42
--- /dev/null
+++ b/src/vscode-docker/create-cortex-config.sh
@@ -0,0 +1,90 @@
+#!/bin/bash
+
+# create-cortex-config.sh
+#
+# Creates cortex.yaml configuration file in the container user's home directory
+# This script runs inside the container and attempts to retrieve GCP metadata
+
+set -o errexit
+set -o nounset
+set -o pipefail
+
+# Wait for metadata server to be ready
+echo "Waiting 5 seconds for metadata server to be ready..."
+sleep 5
+
+if [[ $# -ne 1 ]]; then
+  echo "Usage: $0 <home-directory>"
+  exit 1
+fi
+
+readonly HOME_DIR="${1}"
+readonly CORTEX_CONFIG_PATH="${HOME_DIR}/cortex.yaml"
+
+echo "Creating cortex.yaml configuration..."
+
+# Try to get GCP project ID from metadata server
+# Note: This may not work from inside the container depending on network configuration
+GCP_PROJECT_ID=""
+GCP_REGION=""
+
+if GCP_PROJECT_ID=$(curl --retry 3 --max-time 5 -s -f \
+  -H "Metadata-Flavor: Google" \
+  "http://metadata.google.internal/computeMetadata/v1/project/project-id" 2>/dev/null); then
+  echo "Successfully retrieved GCP project ID: ${GCP_PROJECT_ID}"
+
+  # Also try to get the region
+  if ZONE=$(curl --retry 3 --max-time 5 -s -f \
+    -H "Metadata-Flavor: Google" \
+    "http://metadata.google.internal/computeMetadata/v1/instance/zone" 2>/dev/null); then
+    GCP_REGION=$(echo "${ZONE}" | awk -F'/' '{print $4}' | sed 's/-[^-]*$//')
+    echo "Successfully retrieved GCP region: ${GCP_REGION}"
+  fi
+else
+  echo "Warning: Could not retrieve GCP project ID from metadata server"
+  echo "The metadata server may not be accessible from inside the container"
+
+  # Check if gcloud is available and authenticated as a fallback
+  if command -v gcloud &> /dev/null; then
+    if GCP_PROJECT_ID=$(gcloud config get-value project 2>/dev/null) && [[ -n "${GCP_PROJECT_ID}" ]]; then
+      echo "Retrieved project ID from gcloud config: ${GCP_PROJECT_ID}"
+      GCP_REGION=$(gcloud config get-value compute/region 2>/dev/null || echo "")
+    fi
+  fi
+fi
+
+# Create the cortex.yaml file
+if [[ -n "${GCP_PROJECT_ID}" ]]; then
+  cat > "${CORTEX_CONFIG_PATH}" << EOF
+# Cortex configuration
+# Generated on $(date -u +"%Y-%m-%d %H:%M:%S UTC")
+gcp:
+  project_id: ${GCP_PROJECT_ID}
+EOF
+
+  if [[ -n "${GCP_REGION}" ]]; then
+    cat >> "${CORTEX_CONFIG_PATH}" << EOF
+  region: ${GCP_REGION}
+EOF
+  fi
+
+  echo "cortex.yaml created successfully at ${CORTEX_CONFIG_PATH}"
+  cat "${CORTEX_CONFIG_PATH}"
+else
+  echo "Warning: Could not determine GCP project ID"
+  echo "Creating cortex.yaml with placeholder values"
+  cat > "${CORTEX_CONFIG_PATH}" << EOF
+# Cortex configuration
+# Generated on $(date -u +"%Y-%m-%d %H:%M:%S UTC")
+# WARNING: Could not automatically determine GCP project ID
+gcp:
+  project_id: "UNKNOWN"
+  # Please update this file with the correct project ID
+EOF
+  echo "cortex.yaml created with placeholder at ${CORTEX_CONFIG_PATH}"
+fi
+
+# Ensure proper ownership
+if [[ -f "${CORTEX_CONFIG_PATH}" ]]; then
+  chmod 644 "${CORTEX_CONFIG_PATH}"
+fi

From 970d2d8ecf20607790bc1b19ea3754d584f2f902 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Tue, 24 Feb 2026 19:50:42 +0000
Subject: [PATCH 02/10] modifications to cortex.yaml

---
 src/vscode-docker/create-cortex-config.sh | 18 +++++++-----------
 1 file changed, 7 insertions(+), 11 deletions(-)

diff --git a/src/vscode-docker/create-cortex-config.sh b/src/vscode-docker/create-cortex-config.sh
index 0c61dd42..9579daed 100644
--- a/src/vscode-docker/create-cortex-config.sh
+++ b/src/vscode-docker/create-cortex-config.sh
@@ -58,16 +58,11 @@ if [[ -n "${GCP_PROJECT_ID}" ]]; then
   cat > "${CORTEX_CONFIG_PATH}" << EOF
 # Cortex configuration
 # Generated on $(date -u +"%Y-%m-%d %H:%M:%S UTC")
-gcp:
-  project_id: ${GCP_PROJECT_ID}
+gcp_project_id: ${GCP_PROJECT_ID}
+gcp_region: ${GCP_REGION:-UNKNOWN}
+profiles_repo: shared-artifacts-a2hhlz
 EOF
 
-  if [[ -n "${GCP_REGION}" ]]; then
-    cat >> "${CORTEX_CONFIG_PATH}" << EOF
-  region: ${GCP_REGION}
-EOF
-  fi
-
   echo "cortex.yaml created successfully at ${CORTEX_CONFIG_PATH}"
   cat "${CORTEX_CONFIG_PATH}"
 else
@@ -77,9 +72,10 @@ else
 # Cortex configuration
 # Generated on $(date -u +"%Y-%m-%d %H:%M:%S UTC")
 # WARNING: Could not automatically determine GCP project ID
-gcp:
-  project_id: "UNKNOWN"
-  # Please update this file with the correct project ID
+gcp_project_id: "UNKNOWN"
+gcp_region: "UNKNOWN"
+profiles_repo: shared-artifacts-a2hhlz
+# Please update this file with the correct values
 EOF
   echo "cortex.yaml created with placeholder at ${CORTEX_CONFIG_PATH}"
 fi

From fbdb36bf80c8a8af1a3e2938ab848c53823a87ee Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Tue, 24 Feb 2026 21:57:20 +0000
Subject: [PATCH 03/10] install gh directly from release, avoid apt versioning
 issues

---
 src/vscode-docker/Dockerfile | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/vscode-docker/Dockerfile b/src/vscode-docker/Dockerfile
index 98e0e657..15ee59eb 100644
--- a/src/vscode-docker/Dockerfile
+++ b/src/vscode-docker/Dockerfile
@@ -56,12 +56,10 @@ RUN wget https://go.dev/dl/go1.23.5.linux-amd64.tar.gz && \
     rm go1.23.5.linux-amd64.tar.gz
 
 # Install gh (GitHub CLI version 2.86.0)
-RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg && \
-    chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg && \
-    echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null && \
-    apt-get update && \
-    apt-get install -y gh=2.86.0 && \
-    rm -rf /var/lib/apt/lists/*
+ARG GH_CLI_VERSION=2.86.0
+RUN curl -L "https://github.com/cli/cli/releases/download/v${GH_CLI_VERSION}/gh_${GH_CLI_VERSION}_linux_amd64.tar.gz" -o gh.tar.gz && \
+    tar -xf gh.tar.gz --strip-components=1 -C /usr/local bin/gh && \
+    rm gh.tar.gz
 
 # Install uv (Python package manager version 0.9.27)
 RUN curl -LsSf https://astral.sh/uv/0.9.27/install.sh | sh && \

From 7f18f78124ca34bafd496e6e3aeeea23ff10cfe7 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Tue, 24 Feb 2026 22:19:55 +0000
Subject: [PATCH 04/10] tarball extraction fix

---
 src/vscode-docker/Dockerfile | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/vscode-docker/Dockerfile b/src/vscode-docker/Dockerfile
index 15ee59eb..0c540f4d 100644
--- a/src/vscode-docker/Dockerfile
+++ b/src/vscode-docker/Dockerfile
@@ -58,8 +58,9 @@ RUN wget https://go.dev/dl/go1.23.5.linux-amd64.tar.gz && \
 # Install gh (GitHub CLI version 2.86.0)
 ARG GH_CLI_VERSION=2.86.0
 RUN curl -L "https://github.com/cli/cli/releases/download/v${GH_CLI_VERSION}/gh_${GH_CLI_VERSION}_linux_amd64.tar.gz" -o gh.tar.gz && \
-    tar -xf gh.tar.gz --strip-components=1 -C /usr/local bin/gh && \
-    rm gh.tar.gz
+    tar -xzf gh.tar.gz && \
+    mv gh_${GH_CLI_VERSION}_linux_amd64/bin/gh /usr/local/bin/ && \
+    rm -rf gh.tar.gz gh_${GH_CLI_VERSION}_linux_amd64
 
 # Install uv (Python package manager version 0.9.27)
 RUN curl -LsSf https://astral.sh/uv/0.9.27/install.sh | sh && \

From 8941ed074548736acd2da74e7fdd0902a1c17c79 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Tue, 24 Feb 2026 23:18:49 +0000
Subject: [PATCH 05/10] install cortex-cli as part of startup

---
 src/vscode-docker/.devcontainer.json    |  2 +-
 src/vscode-docker/Dockerfile            |  2 +-
 src/vscode-docker/install-cortex-cli.sh | 75 +++++++++++++++++++++++++
 3 files changed, 77 insertions(+), 2 deletions(-)
 create mode 100644 src/vscode-docker/install-cortex-cli.sh

diff --git a/src/vscode-docker/.devcontainer.json b/src/vscode-docker/.devcontainer.json
index b47feed3..e9e8bf33 100644
--- a/src/vscode-docker/.devcontainer.json
+++ b/src/vscode-docker/.devcontainer.json
@@ -5,7 +5,7 @@
   "shutdownAction": "none",
   "workspaceFolder": "/workspace",
   "postCreateCommand":
-    "./startupscript/post-startup.sh abc /config \"${templateOption:cloud}\" \"${templateOption:login}\"; bash ./create-cortex-config.sh /config",
+    "./startupscript/post-startup.sh abc /config \"${templateOption:cloud}\" \"${templateOption:login}\"; bash ./create-cortex-config.sh /config; bash ./install-cortex-cli.sh",
   // re-mount bucket files on container start up
   "postStartCommand": [
     "./startupscript/remount-on-restart.sh",
diff --git a/src/vscode-docker/Dockerfile b/src/vscode-docker/Dockerfile
index 0c540f4d..2194a26e 100644
--- a/src/vscode-docker/Dockerfile
+++ b/src/vscode-docker/Dockerfile
@@ -68,8 +68,8 @@ RUN curl -LsSf https://astral.sh/uv/0.9.27/install.sh | sh && \
     mv $HOME/.local/bin/uvx /usr/local/bin/
 
 # Set up environment variables
-ENV PATH="/usr/local/go/bin:${PATH}"
 ENV GOPATH="/config/go"
+ENV PATH="/usr/local/go/bin:${GOPATH}/bin:${PATH}"
 ENV GOPRIVATE="github.com/verily-src/*"
 ENV SUDO_PASSWORD="pwd"
 
diff --git a/src/vscode-docker/install-cortex-cli.sh b/src/vscode-docker/install-cortex-cli.sh
new file mode 100644
index 00000000..89b2b856
--- /dev/null
+++ b/src/vscode-docker/install-cortex-cli.sh
@@ -0,0 +1,75 @@
+#!/bin/bash
+
+# install-cortex-cli.sh
+#
+# Installs cortex-cli from the verily1 monorepo if it exists
+# This script runs inside the container after the postCreateCommand
+
+set -o errexit
+set -o nounset
+set -o pipefail
+
+echo "Checking for verily1 monorepo..."
+
+# Check multiple possible locations for verily1 repo
+VERILY1_PATH=""
+for path in "/workspace/repos/verily1" "/config/repos/verily1" "$HOME/repos/verily1"; do
+  if [[ -d "${path}" ]]; then
+    VERILY1_PATH="${path}"
+    break
+  fi
+done
+
+if [[ -z "${VERILY1_PATH}" ]]; then
+  echo "verily1 repository not found in any of the expected locations:"
+  echo "  - /workspace/repos/verily1"
+  echo "  - /config/repos/verily1"
+  echo "  - \$HOME/repos/verily1"
+  echo "Skipping cortex-cli installation"
+  exit 0
+fi
+
+readonly VERILY1_PATH
+
+echo "Found verily1 repository at ${VERILY1_PATH}"
+
+# Verify Go is installed
+if ! command -v go &> /dev/null; then
+  echo "Error: Go is not installed or not in PATH"
+  exit 1
+fi
+
+echo "Go version: $(go version)"
+
+# Set up Go environment if not already set
+export GOPATH="${GOPATH:-/config/go}"
+export PATH="${PATH}:${GOPATH}/bin"
+
+echo "GOPATH: ${GOPATH}"
+echo "Installing cortex-cli..."
+
+# Navigate to verily1 and install cortex-cli
+cd "${VERILY1_PATH}"
+
+if [[ ! -d "cortex/tools/cortex-cli" ]]; then
+  echo "Error: cortex-cli source not found at cortex/tools/cortex-cli"
+  exit 1
+fi
+
+# Install cortex-cli
+if go install ./cortex/tools/cortex-cli; then
+  echo "cortex-cli installed successfully to ${GOPATH}/bin/cortex-cli"
+
+  # Verify installation
+  if [[ -f "${GOPATH}/bin/cortex-cli" ]]; then
+    echo "Verifying cortex-cli installation..."
+    "${GOPATH}/bin/cortex-cli" --help || echo "cortex-cli binary exists but --help failed"
+  else
+    echo "Warning: cortex-cli binary not found at expected location ${GOPATH}/bin/cortex-cli"
+  fi
+else
+  echo "Error: Failed to install cortex-cli"
+  exit 1
+fi
+
+echo "cortex-cli installation complete"

From f4a4305a41e6d5b8ff2a7964b3e254d08ccb9009 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Tue, 24 Feb 2026 23:59:14 +0000
Subject: [PATCH 06/10] install cortex as abc user

---
 src/vscode-docker/install-cortex-cli.sh | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/vscode-docker/install-cortex-cli.sh b/src/vscode-docker/install-cortex-cli.sh
index 89b2b856..f835c4bc 100644
--- a/src/vscode-docker/install-cortex-cli.sh
+++ b/src/vscode-docker/install-cortex-cli.sh
@@ -56,8 +56,9 @@ if [[ ! -d "cortex/tools/cortex-cli" ]]; then
   exit 1
 fi
 
-# Install cortex-cli
-if go install ./cortex/tools/cortex-cli; then
+# Install cortex-cli as user abc (where SSH keys are configured)
+echo "Installing cortex-cli as user abc (root doesn't have SSH keys)..."
+if su - abc -c "export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:\${GOPATH}/bin:\${PATH} && cd ${VERILY1_PATH} && go install ./cortex/tools/cortex-cli"; then
   echo "cortex-cli installed successfully to ${GOPATH}/bin/cortex-cli"
 
   # Verify installation

From d14c315334681ab6d83a604e3b1ab98271aa3d91 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Wed, 25 Feb 2026 18:54:47 +0000
Subject: [PATCH 07/10] verbose output for cortex install

---
 src/vscode-docker/install-cortex-cli.sh | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/vscode-docker/install-cortex-cli.sh b/src/vscode-docker/install-cortex-cli.sh
index f835c4bc..1d2e7f63 100644
--- a/src/vscode-docker/install-cortex-cli.sh
+++ b/src/vscode-docker/install-cortex-cli.sh
@@ -58,7 +58,11 @@ fi
 
 # Install cortex-cli as user abc (where SSH keys are configured)
 echo "Installing cortex-cli as user abc (root doesn't have SSH keys)..."
-if su - abc -c "export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:\${GOPATH}/bin:\${PATH} && cd ${VERILY1_PATH} && go install ./cortex/tools/cortex-cli"; then
+echo "GOPATH is set to: ${GOPATH}"
+echo "Running: su - abc -c 'export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:\${GOPATH}/bin:\${PATH} && cd ${VERILY1_PATH} && go install ./cortex/tools/cortex-cli'"
+
+# Capture both stdout and stderr
+if su - abc -c "export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:\${GOPATH}/bin:\${PATH} && cd ${VERILY1_PATH} && go install ./cortex/tools/cortex-cli" 2>&1; then
   echo "cortex-cli installed successfully to ${GOPATH}/bin/cortex-cli"
 
   # Verify installation
@@ -67,9 +71,13 @@ if su - abc -c "export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:\${GOPA
     "${GOPATH}/bin/cortex-cli" --help || echo "cortex-cli binary exists but --help failed"
   else
     echo "Warning: cortex-cli binary not found at expected location ${GOPATH}/bin/cortex-cli"
+    echo "Checking if it installed elsewhere..."
+    find /config -name "cortex-cli" 2>/dev/null || echo "cortex-cli not found in /config"
   fi
 else
-  echo "Error: Failed to install cortex-cli"
+  EXIT_CODE=$?
+  echo "Error: Failed to install cortex-cli (exit code: ${EXIT_CODE})"
+  echo "The error output should be visible above"
   exit 1
 fi
 

From 7f6a82b274fd51224c0b950736a29de21fb9f445 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Wed, 25 Feb 2026 20:04:55 +0000
Subject: [PATCH 08/10] pipe output from cortex install

---
 src/vscode-docker/install-cortex-cli.sh | 24 ++++++++++++++++++++----
 1 file changed, 20 insertions(+), 4 deletions(-)

diff --git a/src/vscode-docker/install-cortex-cli.sh b/src/vscode-docker/install-cortex-cli.sh
index 1d2e7f63..ac233991 100644
--- a/src/vscode-docker/install-cortex-cli.sh
+++ b/src/vscode-docker/install-cortex-cli.sh
@@ -59,10 +59,23 @@ fi
 # Install cortex-cli as user abc (where SSH keys are configured)
 echo "Installing cortex-cli as user abc (root doesn't have SSH keys)..."
 echo "GOPATH is set to: ${GOPATH}"
-echo "Running: su - abc -c 'export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:\${GOPATH}/bin:\${PATH} && cd ${VERILY1_PATH} && go install ./cortex/tools/cortex-cli'"
 
-# Capture both stdout and stderr
-if su - abc -c "export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:\${GOPATH}/bin:\${PATH} && cd ${VERILY1_PATH} && go install ./cortex/tools/cortex-cli" 2>&1; then
+# Create a temporary script to run as abc user
+# This ensures we capture all output properly
+INSTALL_SCRIPT="/tmp/install-cortex-cli-inner.sh"
+cat > "${INSTALL_SCRIPT}" << 'EOF'
+#!/bin/bash
+set -x  # Show commands being executed
+export GOPATH=/config/go
+export PATH=/usr/local/go/bin:${GOPATH}/bin:${PATH}
+cd /config/repos/verily1
+exec go install ./cortex/tools/cortex-cli 2>&1
+EOF
+
+chmod +x "${INSTALL_SCRIPT}"
+
+echo "Running go install as user abc..."
+if su abc -c "bash ${INSTALL_SCRIPT}"; then
   echo "cortex-cli installed successfully to ${GOPATH}/bin/cortex-cli"
 
   # Verify installation
@@ -74,10 +87,13 @@ if su - abc -c "export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:\${GOPA
     echo "Checking if it installed elsewhere..."
     find /config -name "cortex-cli" 2>/dev/null || echo "cortex-cli not found in /config"
   fi
+
+  rm -f "${INSTALL_SCRIPT}"
 else
   EXIT_CODE=$?
   echo "Error: Failed to install cortex-cli (exit code: ${EXIT_CODE})"
-  echo "The error output should be visible above"
+  echo "Check the output above for errors from go install"
+  rm -f "${INSTALL_SCRIPT}"
   exit 1
 fi
 

From 386c9e1a1d8820f39bc5893871fc846344fc4df3 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Wed, 25 Feb 2026 21:21:48 +0000
Subject: [PATCH 09/10] further attempts to see output from cortex install

---
 src/vscode-docker/install-cortex-cli.sh | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/src/vscode-docker/install-cortex-cli.sh b/src/vscode-docker/install-cortex-cli.sh
index ac233991..e885e3cd 100644
--- a/src/vscode-docker/install-cortex-cli.sh
+++ b/src/vscode-docker/install-cortex-cli.sh
@@ -75,7 +75,18 @@ EOF
 chmod +x "${INSTALL_SCRIPT}"
 
 echo "Running go install as user abc..."
-if su abc -c "bash ${INSTALL_SCRIPT}"; then
+echo "Temp script location: ${INSTALL_SCRIPT}"
+echo "Temp script contents:"
+cat "${INSTALL_SCRIPT}"
+echo "---"
+echo "Testing if user abc exists:"
+id abc || echo "User abc does not exist!"
+echo "Testing if bash exists:"
+which bash || echo "bash not found!"
+echo "Now running the install script..."
+set -x
+if su abc -c "bash ${INSTALL_SCRIPT}" 2>&1; then
+set +x
   echo "cortex-cli installed successfully to ${GOPATH}/bin/cortex-cli"
 
   # Verify installation

From e929ac576fcc0fbda6373221791a905a31a0da87 Mon Sep 17 00:00:00 2001
From: Tucker Reinhardt <reinhardtt@verily.health>
Date: Wed, 25 Feb 2026 21:34:17 +0000
Subject: [PATCH 10/10] run as abc user directly, not su

---
 src/vscode-docker/install-cortex-cli.sh | 36 ++++---------------------
 1 file changed, 5 insertions(+), 31 deletions(-)

diff --git a/src/vscode-docker/install-cortex-cli.sh b/src/vscode-docker/install-cortex-cli.sh
index e885e3cd..a64d5000 100644
--- a/src/vscode-docker/install-cortex-cli.sh
+++ b/src/vscode-docker/install-cortex-cli.sh
@@ -57,36 +57,13 @@ if [[ ! -d "cortex/tools/cortex-cli" ]]; then
 fi
 
 # Install cortex-cli as user abc (where SSH keys are configured)
+# Use the same pattern as post-startup.sh: sudo -u USER bash -l -c
 echo "Installing cortex-cli as user abc (root doesn't have SSH keys)..."
 echo "GOPATH is set to: ${GOPATH}"
+echo "Running go install with verbose output..."
 
-# Create a temporary script to run as abc user
-# This ensures we capture all output properly
-INSTALL_SCRIPT="/tmp/install-cortex-cli-inner.sh"
-cat > "${INSTALL_SCRIPT}" << 'EOF'
-#!/bin/bash
-set -x  # Show commands being executed
-export GOPATH=/config/go
-export PATH=/usr/local/go/bin:${GOPATH}/bin:${PATH}
-cd /config/repos/verily1
-exec go install ./cortex/tools/cortex-cli 2>&1
-EOF
-
-chmod +x "${INSTALL_SCRIPT}"
-
-echo "Running go install as user abc..."
-echo "Temp script location: ${INSTALL_SCRIPT}"
-echo "Temp script contents:"
-cat "${INSTALL_SCRIPT}"
-echo "---"
-echo "Testing if user abc exists:"
-id abc || echo "User abc does not exist!"
-echo "Testing if bash exists:"
-which bash || echo "bash not found!"
-echo "Now running the install script..."
-set -x
-if su abc -c "bash ${INSTALL_SCRIPT}" 2>&1; then
-set +x
+# Use sudo instead of su - matches the RUN_AS_LOGIN_USER pattern from post-startup.sh
+if sudo -u abc bash -l -c "cd ${VERILY1_PATH} && export GOPATH=${GOPATH} && export PATH=/usr/local/go/bin:${GOPATH}/bin:\$PATH && go install -v ./cortex/tools/cortex-cli"; then
   echo "cortex-cli installed successfully to ${GOPATH}/bin/cortex-cli"
 
   # Verify installation
@@ -98,13 +75,10 @@ set +x
     echo "Checking if it installed elsewhere..."
     find /config -name "cortex-cli" 2>/dev/null || echo "cortex-cli not found in /config"
   fi
-
-  rm -f "${INSTALL_SCRIPT}"
 else
   EXIT_CODE=$?
   echo "Error: Failed to install cortex-cli (exit code: ${EXIT_CODE})"
-  echo "Check the output above for errors from go install"
-  rm -f "${INSTALL_SCRIPT}"
+  echo "Error output should be visible above"
   exit 1
 fi