supercharge codebase-memory-mcp: streamline and consolidate api, autoindexing, PageRank, dependency indexing, speedup, cli config, autotune

.clangd

@@ -0,0 +1,36 @@
+# clangd configuration for codebase-memory-mcp
+#
+# Mirrors the include paths and defines from Makefile.cbm CFLAGS_COMMON so
+# clangd can resolve all headers without needing compile_commands.json.
+# Paths are relative to the project root (where this file lives).
+#
+# Works with both clang (macOS/Linux) and gcc — clangd uses these flags
+# directly regardless of which compiler is selected for the build.
+
+CompileFlags:
+  Add:
+    - -std=c11
+    - -D_DEFAULT_SOURCE
+    # Project source headers
+    - -Isrc
+    # Vendored libraries: yyjson, xxhash, sqlite3 wrappers
+    - -Ivendored
+    - -Ivendored/sqlite3
+    - -Ivendored/mimalloc/include
+    # Internal cbm extraction layer and tree-sitter runtime
+    - -Iinternal/cbm
+    - -Iinternal/cbm/vendored/ts_runtime/include
+  # Remove flags clangd cannot handle (sanitizer, link flags)
+  Remove:
+    - -fsanitize=*
+    - -fno-omit-frame-pointer
+    - -lstdc++
+    - -lpthread
+    - -lm
+    - -lz
+
+Diagnostics:
+  # Suppress false-positive "implicit declaration" warnings caused by
+  # clangd analysing files in isolation without the full TU context.
+  Suppress:
+    - pp_file_not_found

.gitignore

@@ -22,6 +22,16 @@ coverage.txt
 .DS_Store
 Thumbs.db
 
+# Git worktrees (created by Claude Code subagents)
+.worktrees/
+
+# Runtime/session artifacts
+session_project
+project
+project|params.project
+conductor/
+with
+
 # Database files (local cache)
 *.db
 *.db-wal
@@ -33,6 +43,7 @@ Thumbs.db
 # Local project memory (Claude Code auto-memory)
 memory/
 reference/
+.claude/
 
 # Build artifacts
 build/
@@ -42,3 +53,4 @@ graph-ui/dist/
 # Generated reports
 BENCHMARK_REPORT.md
 TEST_PLAN.md
+scripts/autotune_results.json

.mcp.json

@@ -1,8 +1,8 @@
 {
   "mcpServers": {
     "codebase-memory-mcp": {
-      "command": "/Users/martinvogel/.local/bin/codebase-memory-mcp",
-      "args": []
+      "command": "sh",
+      "args": ["-c", "exec $HOME/.local/bin/codebase-memory-mcp"]
     }
   }
 }

CLAUDE.md

@@ -0,0 +1,34 @@
+# codebase-memory-mcp — Developer Notes for Claude
+
+## Build & Test (C server)
+
+All C targets use `Makefile.cbm`:
+
+```bash
+make -f Makefile.cbm test          # build + run full test suite (ASan/UBSan)
+make -f Makefile.cbm test-leak     # heap leak check (see below)
+make -f Makefile.cbm test-analyze  # Clang static analyzer (requires clang, not gcc)
+```
+
+## Memory Leak Testing
+
+**macOS** — uses Apple's `leaks --atExit` on a separate ASan-free binary:
+```bash
+make -f Makefile.cbm test-leak
+# Report saved to build/c/leak-report.txt
+# Target line: "Process NNNNN: 0 leaks for 0 total leaked bytes."
+```
+
+**Linux** — uses LSan via ASan env var on the regular test runner:
+```bash
+make -f Makefile.cbm test-leak
+# Report saved to build/c/leak-report.txt
+# Exit 0 = no leaks.
+```
+
+Why a separate binary on macOS: `leaks` cannot inspect processes that use a custom malloc (ASan replaces it). The `test-runner-nosan` target rebuilds without `-fsanitize` flags specifically for this purpose.
+
+## Project Structure (C server)
+
+Sources live under `src/`; tests under `tests/`; vendored C libs under `vendored/`.
+The Go layer (`cmd/`, `internal/`) wraps the C server via CGO — see `CONTRIBUTING.md` for the Go side.

CONTRIBUTING.md

@@ -26,6 +26,30 @@ Key test files:
 - `internal/pipeline/astdump_test.go` — 90+ AST structure cases
 - `internal/pipeline/pipeline_test.go` — integration tests
 
+## Run C Server Tests
+
+The MCP server core is written in C and has its own test suite under `tests/`:
+
+```bash
+make -f Makefile.cbm test          # full suite with ASan + UBSan
+make -f Makefile.cbm test-leak     # heap leak check (see below)
+make -f Makefile.cbm test-analyze  # Clang static analyzer (requires clang, not gcc)
+```
+
+**Memory leak detection:**
+
+On **macOS**, `test-leak` builds a sanitizer-free binary (`test-runner-nosan`) and runs Apple's
+`leaks --atExit` on it. ASan replaces malloc, so the standard `test-runner` cannot be inspected
+by `leaks` — the separate nosan build is required.
+
+On **Linux**, `test-leak` runs the regular `test-runner` with `ASAN_OPTIONS=detect_leaks=1` to
+activate LSan.
+
+In both cases the full report is written to `build/c/leak-report.txt`. A clean run ends with:
+```
+Process NNNNN: 0 leaks for 0 total leaked bytes.
+```
+
 ## Run Linter
 
 ```bash