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server that indexes codebases into an AST knowledge graph with semantic search, call graph traversal, and HTTP route tracing","maintainers":[{"name":"sdsrs","email":"jack.sds5889@gmail.com"}],"readme":"# code-graph-mcp\n\nA high-performance code knowledge graph server implementing the [Model Context Protocol (MCP)](https://modelcontextprotocol.io/). Indexes codebases into a structured AST knowledge graph with semantic search, call graph traversal, and HTTP route tracing — designed to give AI coding assistants deep, structured understanding of your code.\n\n## Features\n\n- **Multi-language parsing** — Tree-sitter AST extraction across tiers of depth:\n  - **Full** (calls + imports + inheritance + HTTP routes + test markers): TypeScript/TSX, JavaScript, Go, Python, Rust, Java\n  - **Smoke-tested** (calls + imports + inheritance): C#, Kotlin, Ruby, PHP, Swift, Dart\n  - **Limited** (functions + calls + `#include` imports + gtest test markers; `Class::method` scope qualification deferred): C, C++\n  - **Scripting**: Bash (functions + commands + `source`/`.` imports), Markdown (headings)\n  - **File-FTS only** (no AST symbol extraction): HTML, CSS, JSON\n- **Semantic code search** — Hybrid BM25 full-text + vector semantic search with Reciprocal Rank Fusion (RRF), powered by sqlite-vec\n- **Call graph traversal** — Recursive CTE queries to trace callers/callees with cycle detection\n- **HTTP route tracing** — Map route paths to backend handler functions (Express, Flask/FastAPI, Go `net/http`)\n- **Dead code detection** — Find unreferenced symbols with smart Orphan/Exported-Unused classification\n- **Impact analysis** — Determine the blast radius of code changes by tracing all dependents\n- **Incremental indexing** — Merkle tree change detection with file system watcher for real-time updates. Smart event filtering skips metadata-only changes (chmod, xattr)\n- **Context compression** — Token-aware snippet extraction for LLM context windows (L0→full code, L1→summaries, L2→file groups, L3→directory overview). Compact JSON output saves 15-20% tokens\n- **Embedding model** — Optional local embedding via Candle (feature-gated `embed-model`). Context reordered to prioritize structural relations over code for better embedding quality\n- **Self-healing** — Automatic SQLite corruption recovery with rebuild. Startup repair for incomplete indexing (Phase 3 failures)\n- **MCP protocol** — JSON-RPC 2.0 over stdio, plug-and-play with Claude Code, Cursor, Windsurf, and other MCP clients\n- **Claude Code Plugin** — First-class plugin with slash commands (`/understand`, `/trace`, `/impact`), agents, skills, auto-indexing hooks, StatusLine integration, and self-updating\n\n## Why code-graph-mcp?\n\nUnlike naive full-text search or simple AST dumps, code-graph-mcp builds a **structured knowledge graph** that understands the relationships between symbols across your entire codebase.\n\n### Incremental by Design\n\nBLAKE3 Merkle tree tracks every file's content hash. On re-index, only changed files are re-parsed — unchanged directory subtrees are skipped entirely via mtime cache. When a function signature changes, **dirty propagation** automatically regenerates context for all downstream callers across files.\n\n### Hybrid Search, Not Just Grep\n\nCombines BM25 full-text ranking (FTS5) with vector semantic similarity (sqlite-vec) via **Reciprocal Rank Fusion (RRF)** with raw score blending — so searching \"handle user login\" finds the right function even if it's named `authenticate_session`. Results are auto-compressed to fit LLM context windows.\n\n### Scope-Aware Relation Extraction\n\nThe parser doesn't just find function calls — it tracks them within their proper scope context. Extracts calls, imports, inheritance, interface implementations, exports, and HTTP route bindings. Same-file targets are preferred over cross-file matches to minimize false-positive edges.\n\n### HTTP Request Flow Tracing\n\nUnique to code-graph-mcp: trace from `GET /api/users` → route handler → service layer → database call in a single query. Supports Express, Flask/FastAPI, and Go HTTP frameworks.\n\n### Zero External Dependencies at Runtime\n\nSingle binary, embedded SQLite, bundled sqlite-vec extension, optional local embedding model via Candle — no database server, no cloud API, no Docker required. Runs entirely on your machine.\n\n### Built for AI Assistants\n\nEvery design decision — from token-aware compression to node_id-based snippet expansion — is optimized for LLM context windows. Works out of the box with Claude Code, Cursor, Windsurf, and any MCP-compatible client.\n\n## Performance\n\n| Metric | Value |\n|--------|-------|\n| Indexing speed | **300+ files/second** (single-threaded, release build) |\n| Incremental re-index | **<250ms** no-change detection via BLAKE3 Merkle tree |\n| FTS search P50 / P99 | **<300us / <1ms** |\n| Database overhead | **~3.5MB** per 800 nodes |\n| Token savings | **5-20x fewer tokens** per code understanding task vs grep+read |\n\nRun `code-graph-mcp benchmark` on your own project to measure.\n\n## Efficiency: code-graph vs Traditional Tools\n\nReal-world benchmarks comparing code-graph-mcp tools against traditional approaches (Grep + Read + Glob) on a 33-file Rust project (~537 AST nodes).\n\n### Tool Call Reduction\n\n| Scenario | Traditional | code-graph | Savings |\n|----------|:-----------:|:----------:|:-------:|\n| Project architecture overview | 5-8 calls | 1 call (`project_map`) | **~85%** |\n| Find function by concept | 3-5 calls | 1 call (`semantic_code_search`) | **~75%** |\n| Trace 2-level call chain | 8-15 calls | 1 call (`get_call_graph`) | **~90%** |\n| Pre-change impact analysis | 10-20+ calls | 1 call (`impact_analysis`) | **~95%** |\n| Module structure & exports | 5+ calls | 1 call (`module_overview`) | **~80%** |\n| File dependency mapping | 3-5 calls | 1 call (`dependency_graph`) | **~75%** |\n| Similar code detection | N/A | 1 call (`find_similar_code`) | **unique** |\n\n### Overall Session Efficiency\n\n| Metric | Without code-graph | With code-graph | Improvement |\n|--------|:------------------:|:---------------:|:-----------:|\n| Tool calls per navigation task | ~6 | ~1.2 | **~80% fewer** |\n| Source lines read into context | ~8,000 lines | ~400 lines (structured) | **~95% less** |\n| Navigation token cost | ~36K tokens | ~7K tokens | **~80% saved** |\n| Full session token savings | — | — | **40-60%** |\n\n### What code-graph Uniquely Enables\n\n- **Impact analysis** — \"Changing `conn` affects 33 functions across 4 files, 78 tests at HIGH risk\" — impossible to derive manually with Grep\n- **Transitive call tracing** — Follow `main` → `run_serve` → `handle_message` → `handle_tools_call` → `conn` in one query\n- **Semantic search** — Find `authenticate_session` when searching \"handle user login\"\n- **Dependency strength** — Not just \"file A imports file B\", but \"file A uses 38 symbols from file B\"\n\n### When Traditional Tools Are Still Better\n\n| Use Case | Best Tool |\n|----------|-----------|\n| Exact string / constant search | Grep |\n| Reading a file to edit it | Read |\n| Finding files by name pattern | Glob |\n\n## Architecture\n\n```\nsrc/\n├── domain.rs     # Shared constants, relation types, env-var config\n├── mcp/          # MCP protocol layer (JSON-RPC, tool registry, server)\n│   └── server/   # McpServer with IndexingState + CacheState sub-structs\n├── parser/       # Tree-sitter parsing, relation extraction, LanguageConfig dispatch\n├── indexer/      # 3-phase pipeline, Merkle tree, file watcher\n├── storage/      # SQLite schema (v6), CRUD, FTS5, migrations\n├── graph/        # Recursive CTE call graph queries\n├── search/       # RRF fusion search combining BM25 + vector\n├── embedding/    # Candle embedding model (optional, masked mean pooling)\n├── sandbox/      # Context compressor with token estimation\n└── utils/        # Language detection, config\n```\n\n## Installation\n\n### Option 1: Claude Code Plugin (Recommended)\n\nInstall as a Claude Code plugin for the best experience — includes slash commands, agents, skills, auto-indexing hooks, StatusLine health display, and automatic updates:\n\n```bash\n# Step 1: Add the marketplace\n/plugin marketplace add sdsrss/code-graph-mcp\n\n# Step 2: Install the plugin\n/plugin install code-graph-mcp\n```\n\nWhat you get:\n- **MCP Server** — All code-graph tools available to Claude\n- **Slash Commands** — `/understand <module>`, `/trace <route>`, `/impact <symbol>`\n- **Code Explorer Agent** — Deep code understanding expert via `code-explorer`\n- **Auto-indexing Hook** — Incremental index on every file edit (PostToolUse)\n- **StatusLine** — Real-time health display (nodes, files, watch status) — compatible with other plugins' StatusLine via composite multiplexer\n- **Auto-update** — Checks for new versions every 6h, updates silently\n\n#### Manual Update\n\n```bash\nnpm update -g @sdsrs/code-graph\n```\n\nThen reconnect the MCP server in Claude Code with `/mcp`.\n\n> **Note:** Auto-update is disabled in the source repo directory (dev mode). Use manual update when developing the plugin itself.\n\n#### Invited-memory mode (quieter prompts)\n\nBy default, every user prompt the plugin deems code-related gets a small context injection from `code-graph` CLI output. If you'd rather rely on MEMORY.md + explicit tool calls, opt into invited-memory mode:\n\n1. Adopt the plugin contract into your project's memory index (idempotent, self-heals):\n   ```bash\n   code-graph-mcp adopt\n   ```\n   This writes `plugin_code_graph_mcp.md` (decision rules) into `~/.claude/projects/<slug>/memory/` and links it from `MEMORY.md` inside a sentinel block. Run `code-graph-mcp unadopt` to remove.\n2. Set the activation env var in `~/.claude/settings.json`:\n   ```json\n   {\n     \"env\": { \"CODE_GRAPH_QUIET_HOOKS\": \"1\" }\n   }\n   ```\n3. Restart Claude Code. Session startup skips the project-map injection, UserPromptSubmit stops auto-injecting context, and the MCP `instructions` become a short pointer to the MEMORY.md file.\n\n### Option 2: Claude Code MCP Server Only\n\nRegister as an MCP server without the plugin features:\n\n```bash\nclaude mcp add code-graph-mcp -- npx -y @sdsrs/code-graph\n```\n\n### Option 3: Cursor / Windsurf / Other MCP Clients\n\nAdd to your MCP settings file (e.g. `~/.cursor/mcp.json`):\n\n```json\n{\n  \"mcpServers\": {\n    \"code-graph\": {\n      \"command\": \"npx\",\n      \"args\": [\"-y\", \"@sdsrs/code-graph\"]\n    }\n  }\n}\n```\n\n### Option 4: npx (No Install)\n\nRun directly without installing:\n\n```bash\nnpx -y @sdsrs/code-graph\n```\n\n### Option 5: npm (Global Install)\n\nInstall globally, then run anywhere:\n\n```bash\nnpm install -g @sdsrs/code-graph\ncode-graph-mcp\n```\n\n## Uninstallation\n\n### Claude Code Plugin\n\n```bash\n# Uninstall the plugin\n/plugin uninstall code-graph-mcp\n\n# (Optional) Remove the marketplace\n/plugin marketplace remove code-graph-mcp\n\n# (Optional) Clean up all config and cache data\nnode ~/.claude/plugins/cache/code-graph-mcp/code-graph-mcp/*/scripts/lifecycle.js uninstall\n```\n\n### Claude Code MCP Server\n\n```bash\nclaude mcp remove code-graph-mcp\n```\n\n### Cursor / Windsurf / Other MCP Clients\n\nRemove the `code-graph` entry from your MCP settings file (e.g. `~/.cursor/mcp.json`).\n\n### npm (Global)\n\n```bash\nnpm uninstall -g @sdsrs/code-graph\n```\n\n## MCP Tools\n\n| Tool | Description |\n|------|-------------|\n| `project_map` | Full project architecture: modules, dependencies, entry points, hot functions |\n| `semantic_code_search` | Hybrid BM25 + vector + graph search for AST nodes |\n| `get_call_graph` | Trace upstream/downstream call chains for a function |\n| `trace_http_chain` | Full request flow: route → handler → downstream call chain |\n| `impact_analysis` | Analyze the blast radius of changing a symbol |\n| `module_overview` | High-level overview of a module's structure and exports |\n| `dependency_graph` | Visualize dependency relationships between modules. Supports `compact` mode |\n| `find_similar_code` | Find semantically similar code via embeddings. Requires `symbol_name` or `node_id` |\n| `get_ast_node` | Extract a specific code symbol with signature, body, and relations. Supports `compact` mode |\n| `ast_search` | Search AST nodes by text and/or structural filters (type, return type, params) |\n| `find_references` | Find all references to a symbol (callers, importers, inheritors). Supports `compact` mode |\n| `find_dead_code` | Find unused code — orphan symbols and exported-but-unused public APIs |\n\n## CLI Commands\n\nAll tools are also available as CLI subcommands for shell scripts, hooks, and terminal workflows:\n\n| Command | MCP Equivalent | Description |\n|---------|---------------|-------------|\n| `search <query>` | `semantic_code_search` | FTS5 search by concept |\n| `ast-search [query]` | `ast_search` | Structural search with `--type`/`--returns`/`--params` filters |\n| `callgraph <symbol>` | `get_call_graph` | Show call graph (callers/callees) |\n| `impact <symbol>` | `impact_analysis` | Impact analysis (callers, routes, risk level) |\n| `show <symbol>` | `get_ast_node` | Show symbol details (code, type, signature) |\n| `map` | `project_map` | Project architecture map |\n| `overview <path>` | `module_overview` | Module symbols grouped by file and type |\n| `deps <file>` | `dependency_graph` | File-level dependency graph |\n| `trace <route>` | `trace_http_chain` | Trace HTTP route → handler → downstream calls |\n| `similar <symbol>` | `find_similar_code` | Find semantically similar code (requires embeddings) |\n| `refs <symbol>` | `find_references` | Find all references to a symbol |\n| `dead-code [path]` | `find_dead_code` | Find unused code (orphans and exported-unused) |\n| `grep <pattern>` | — | AST-context grep (ripgrep + containing function/class) |\n| `incremental-index` | — | Run incremental index update (auto-creates DB if needed) |\n| `health-check` | `get_index_status` | Query index status and freshness |\n| `benchmark` | — | Benchmark index speed, query latency, token savings |\n\nCommon options: `--json` (JSON output), `--compact` (compact output), `--limit N`, `--depth N`, `--file <path>`.\n\n## Plugin Slash Commands\n\nAvailable when installed as a Claude Code plugin:\n\n| Command | Description |\n|---------|-------------|\n| `/understand <module>` | Deep dive into a module or file's architecture and relationships |\n| `/trace <route>` | Trace a full HTTP request flow from route to data layer |\n| `/impact <symbol>` | Analyze the impact scope of changing a symbol before modifying it |\n| `/status` | Show code-graph index status and embedding progress |\n| `/rebuild` | Force a full code-graph index rebuild |\n\n## Supported Languages (16)\n\n| Language | Extensions | Relations Extracted |\n|----------|-----------|-------------------|\n| TypeScript | .ts, .tsx | calls, imports, exports, inherits, implements, routes_to |\n| JavaScript | .js, .jsx, .mjs, .cjs | calls, imports, exports, inherits, routes_to |\n| Go | .go | calls, imports, routes_to |\n| Python | .py, .pyi | calls, imports, inherits, routes_to |\n| Rust | .rs | calls, imports, inherits, implements |\n| Java | .java | calls, imports, inherits, implements |\n| C# | .cs | calls, imports, inherits, implements |\n| Kotlin | .kt, .kts | calls, imports, inherits |\n| Ruby | .rb | calls, imports, inherits |\n| PHP | .php | calls, imports, inherits, implements |\n| Swift | .swift | calls, imports, inherits |\n| Dart | .dart | calls, imports, implements |\n| C | .c, .h | calls, imports |\n| C++ | .cpp, .cc, .cxx, .hpp | calls, imports, inherits |\n| HTML | .html, .htm | structural parsing |\n| CSS | .css | structural parsing |\n\n## Team-shared graph snapshot\n\nSkip the full local index for team members and CI runners by publishing a\n~3-5MB graph snapshot with each GitHub release.\n\n**Setup (one-time):**\n1. Copy `node_modules/code-graph-mcp/templates/code-graph-snapshot.yml`\n   into your repo's `.github/workflows/`.\n2. Push a release tag. The workflow uploads\n   `code-graph-snapshot-<sha>.db.zst` as a release asset.\n\n**Verify:**\n\n```bash\nnpx code-graph-mcp snapshot inspect ./code-graph-snapshot-<sha>.db.zst\n```\n\nAfter setup, fresh clones automatically fetch the latest snapshot the\nfirst time the MCP server starts. No client-side configuration needed.\n\n## Storage\n\nUses SQLite with:\n- FTS5 for full-text search\n- sqlite-vec extension for vector similarity search\n- Merkle tree hashes for incremental change detection\n\nData is stored in `.code-graph/index.db` under the project root (auto-created, gitignored).\n\n## Build from Source\n\n### Prerequisites\n\n- Rust 1.75+ (2021 edition)\n- A C compiler (for bundled SQLite / sqlite-vec)\n\n### Build\n\n```bash\n# Default build — FTS5-only (~10 MB binary, no embedding model)\ncargo build --release\n\n# With local embedding model (~150 MB binary; downloads ~120 MB model lazily on first semantic search)\ncargo build --release --features embed-model\n```\n\n> Direct `cargo install` users get the FTS5-only build by default. npm/npx/plugin\n> users get the full hybrid (FTS5 + vector) build automatically — release CI\n> compiles with `--features embed-model` for shipped binaries.\n\n### Configure (from source)\n\nAdd the compiled binary to your MCP settings:\n\n```json\n{\n  \"mcpServers\": {\n    \"code-graph\": {\n      \"command\": \"/path/to/target/release/code-graph-mcp\"\n    }\n  }\n}\n```\n\n## Development\n\n```bash\n# Run tests\ncargo test\n\n# Run tests without embedding model\ncargo test --no-default-features\n\n# Check compilation\ncargo check\n\n# Run performance benchmarks (indexing, search, call graph)\ncargo bench --no-default-features\n```\n\n## License\n\nSee [LICENSE](LICENSE) for details.\n","readmeFilename":"README.md"}