From 69e14f3ca291c0963617e1f56ddcc87e926aef5d Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 11 Jun 2026 07:47:25 +0000
Subject: [PATCH 1/3] feat: add shared/mcp/codebase-memory-mcp.md with
 cache-hosted incremental index

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 .../shared/mcp/codebase-memory-mcp.md         | 154 ++++++++++++++++++
 1 file changed, 154 insertions(+)
 create mode 100644 .github/workflows/shared/mcp/codebase-memory-mcp.md

diff --git a/.github/workflows/shared/mcp/codebase-memory-mcp.md b/.github/workflows/shared/mcp/codebase-memory-mcp.md
new file mode 100644
index 00000000000..b716f76c445
--- /dev/null
+++ b/.github/workflows/shared/mcp/codebase-memory-mcp.md
@@ -0,0 +1,154 @@
+---
+# Codebase Memory MCP — Structural Code Intelligence
+# Wraps the codebase-memory-mcp server for fast code-graph queries,
+# semantic search, and architecture analysis across 159 languages.
+# The knowledge-graph index is stored in cache-memory so it survives
+# between workflow runs; only incremental re-indexing is needed after that.
+#
+# See: https://github.com/DeusData/codebase-memory-mcp
+#
+# Usage:
+#   network:
+#     allowed:
+#       - node                     # Required for npm install -g codebase-memory-mcp
+#   tools:
+#     cache-memory: true           # REQUIRED: already set by this import
+#   imports:
+#     - shared/mcp/codebase-memory-mcp.md
+
+tools:
+  cache-memory: true
+
+mcp-servers:
+  codebase-memory:
+    command: "codebase-memory-mcp"
+    args: []
+    allowed:
+      - index_repository
+      - index_status
+      - list_projects
+      - search_graph
+      - trace_path
+      - detect_changes
+      - query_graph
+      - get_graph_schema
+      - get_code_snippet
+      - get_architecture
+      - search_code
+      - ingest_traces
+
+steps:
+  - name: Install codebase-memory-mcp
+    run: |
+      npm install -g codebase-memory-mcp
+
+  - name: Set up codebase-memory index cache
+    run: |
+      # Symlink ~/.cache/codebase-memory-mcp into cache-memory so the SQLite
+      # knowledge-graph index persists automatically across workflow runs.
+      mkdir -p /tmp/gh-aw/cache-memory/codebase-memory-mcp-store
+      mkdir -p ~/.cache
+
+      if [ ! -e ~/.cache/codebase-memory-mcp ]; then
+        ln -s /tmp/gh-aw/cache-memory/codebase-memory-mcp-store ~/.cache/codebase-memory-mcp
+        echo "🔗 Created ~/.cache/codebase-memory-mcp → cache-memory/codebase-memory-mcp-store"
+      elif [ -d ~/.cache/codebase-memory-mcp ] && [ ! -L ~/.cache/codebase-memory-mcp ]; then
+        # Plain directory present (e.g. first run after adding this import) — migrate
+        cp -r ~/.cache/codebase-memory-mcp/. /tmp/gh-aw/cache-memory/codebase-memory-mcp-store/ 2>/dev/null || true
+        rm -rf ~/.cache/codebase-memory-mcp
+        ln -s /tmp/gh-aw/cache-memory/codebase-memory-mcp-store ~/.cache/codebase-memory-mcp
+        echo "🔗 Migrated existing store → cache-memory/codebase-memory-mcp-store"
+      else
+        echo "✅ ~/.cache/codebase-memory-mcp already linked to cache-memory store"
+      fi
+
+  - name: Index repository (incremental)
+    run: |
+      # Index or incrementally update the knowledge graph.
+      # On the first run a full graph is built; subsequent runs detect the
+      # existing store and only re-index changed files (git-diff-driven).
+      echo "Indexing ${GITHUB_WORKSPACE}..."
+      codebase-memory-mcp cli index_repository "{\"repo_path\": \"${GITHUB_WORKSPACE}\"}"
+      codebase-memory-mcp cli index_status "{\"repo_path\": \"${GITHUB_WORKSPACE}\"}" || true
+      echo "✅ Codebase memory index ready"
+---
+
+<!--
+## Codebase Memory MCP
+
+Provides fast structural code intelligence via codebase-memory-mcp with
+159-language tree-sitter parsing, Hybrid LSP semantic type resolution, and
+a persistent SQLite knowledge graph backed by GitHub Actions cache-memory.
+The graph is built on the first run and updated incrementally on subsequent runs.
+
+Documentation: https://github.com/DeusData/codebase-memory-mcp
+
+## Available Tools
+
+The following read-oriented tools are enabled by default:
+
+- `index_repository` — Full or incremental index of the workspace
+- `index_status` — Indexing status and node/edge counts for a project
+- `list_projects` — All indexed projects with node/edge counts
+- `search_graph` — Structural search by label, name pattern, file pattern, or degree
+- `trace_path` — BFS call-graph traversal (inbound/outbound/both, depth 1–5)
+- `detect_changes` — Map git diff to affected symbols with risk classification
+- `query_graph` — Read-only openCypher-like graph queries (`MATCH`, `WHERE`, `RETURN`, ...)
+- `get_graph_schema` — Node/edge schema, counts, and property definitions
+- `get_code_snippet` — Retrieve source for a function by qualified name
+- `get_architecture` — Architecture overview: languages, packages, routes, clusters, ADR
+- `search_code` — Grep-like text search over indexed project files
+- `ingest_traces` — Ingest runtime traces to validate `HTTP_CALLS` edges
+
+## Excluded Write Tools
+
+These tools are excluded from the default allowlist:
+
+- `delete_project` — Permanently removes a project and all graph data
+- `manage_adr` — Creates, updates, and deletes Architecture Decision Records
+
+To enable `manage_adr`, add it explicitly in the importing workflow:
+
+```yaml
+mcp-servers:
+  codebase-memory:
+    allowed:
+      - manage_adr
+```
+
+## Persistence
+
+The knowledge-graph index lives at
+`/tmp/gh-aw/cache-memory/codebase-memory-mcp-store/` (symlinked from
+`~/.cache/codebase-memory-mcp/`). The `cache-memory` tool saves and restores
+this directory across runs automatically.
+
+## Requirements
+
+The importing workflow must include:
+
+- `node` in `network.allowed` — needed for `npm install -g codebase-memory-mcp`
+- `tools.cache-memory: true` — already set by this import; do not disable it
+
+## Example Queries
+
+```
+# Architecture overview (entry points, routes, hotspots, clusters)
+get_architecture {}
+
+# Find all HTTP handler functions
+search_graph {"label": "Function", "name_pattern": ".*Handler.*"}
+
+# Trace callers of a function, depth 3
+trace_path {"function_name": "ProcessOrder", "direction": "inbound", "depth": 3}
+
+# Cypher query — functions that call a specific method
+query_graph {"query": "MATCH (f:Function)-[:CALLS]->(g:Function) WHERE g.name = 'SaveRecord' RETURN f.name LIMIT 20"}
+
+# Symbols affected by the current git diff
+detect_changes {"repo_path": "."}
+
+# Text search within indexed files
+search_code {"query": "TODO", "file_pattern": "*.go"}
+```
+-->

From 09e48dea03f92358fcd82df366e2b6fb954d4e75 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 11 Jun 2026 07:48:19 +0000
Subject: [PATCH 2/3] fix: improve error handling and diagnostic output in
 codebase-memory-mcp setup steps

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 .../workflows/shared/mcp/codebase-memory-mcp.md    | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/shared/mcp/codebase-memory-mcp.md b/.github/workflows/shared/mcp/codebase-memory-mcp.md
index b716f76c445..30650fb7b07 100644
--- a/.github/workflows/shared/mcp/codebase-memory-mcp.md
+++ b/.github/workflows/shared/mcp/codebase-memory-mcp.md
@@ -54,7 +54,9 @@ steps:
         echo "🔗 Created ~/.cache/codebase-memory-mcp → cache-memory/codebase-memory-mcp-store"
       elif [ -d ~/.cache/codebase-memory-mcp ] && [ ! -L ~/.cache/codebase-memory-mcp ]; then
         # Plain directory present (e.g. first run after adding this import) — migrate
-        cp -r ~/.cache/codebase-memory-mcp/. /tmp/gh-aw/cache-memory/codebase-memory-mcp-store/ 2>/dev/null || true
+        if ! cp -r ~/.cache/codebase-memory-mcp/. /tmp/gh-aw/cache-memory/codebase-memory-mcp-store/ 2>&1; then
+          echo "warning: migration copy failed; the existing store may be incomplete. Starting fresh." >&2
+        fi
         rm -rf ~/.cache/codebase-memory-mcp
         ln -s /tmp/gh-aw/cache-memory/codebase-memory-mcp-store ~/.cache/codebase-memory-mcp
         echo "🔗 Migrated existing store → cache-memory/codebase-memory-mcp-store"
@@ -68,8 +70,14 @@ steps:
       # On the first run a full graph is built; subsequent runs detect the
       # existing store and only re-index changed files (git-diff-driven).
       echo "Indexing ${GITHUB_WORKSPACE}..."
-      codebase-memory-mcp cli index_repository "{\"repo_path\": \"${GITHUB_WORKSPACE}\"}"
-      codebase-memory-mcp cli index_status "{\"repo_path\": \"${GITHUB_WORKSPACE}\"}" || true
+      if ! codebase-memory-mcp cli index_repository "{\"repo_path\": \"${GITHUB_WORKSPACE}\"}" 2>&1; then
+        echo "error: index_repository failed — check the output above for details." >&2
+        exit 1
+      fi
+      # index_status is best-effort: the server may not yet have flushed all
+      # metadata, so a non-zero exit here is not a fatal condition.
+      codebase-memory-mcp cli index_status "{\"repo_path\": \"${GITHUB_WORKSPACE}\"}" 2>&1 || \
+        echo "warning: index_status returned a non-zero exit code (non-fatal)"
       echo "✅ Codebase memory index ready"
 ---
 

From 128e24deb15e10670887b0431c52fbf51ab4c316 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 11 Jun 2026 12:01:26 +0000
Subject: [PATCH 3/3] fix: pin codebase-memory-mcp to 0.7.0, disable npm
 scripts during install

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 .github/workflows/shared/mcp/codebase-memory-mcp.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/shared/mcp/codebase-memory-mcp.md b/.github/workflows/shared/mcp/codebase-memory-mcp.md
index 30650fb7b07..45c6f7e230b 100644
--- a/.github/workflows/shared/mcp/codebase-memory-mcp.md
+++ b/.github/workflows/shared/mcp/codebase-memory-mcp.md
@@ -40,7 +40,9 @@ mcp-servers:
 steps:
   - name: Install codebase-memory-mcp
     run: |
-      npm install -g codebase-memory-mcp
+      npm install -g codebase-memory-mcp@0.7.0 --ignore-scripts
+      # Explicitly run the binary-download postinstall after reviewing it above.
+      node "$(npm root -g)/codebase-memory-mcp/install.js"
 
   - name: Set up codebase-memory index cache
     run: |