code-graph-mcp

A high-performance code knowledge graph server implementing the Model Context Protocol (MCP). 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.

Features

• Multi-language parsing — Tree-sitter AST extraction for 16 languages: TypeScript, JavaScript, Go, Python, Rust, Java, C, C++, C#, Kotlin, Ruby, PHP, Swift, Dart, HTML, CSS
• Semantic code search — Hybrid BM25 full-text + vector semantic search with Reciprocal Rank Fusion (RRF), powered by sqlite-vec
• Call graph traversal — Recursive CTE queries to trace callers/callees with cycle detection
• HTTP route tracing — Map route paths to backend handler functions (Express, Flask/FastAPI, Go net/http)
• Dead code detection — Find unreferenced symbols with smart Orphan/Exported-Unused classification
• Impact analysis — Determine the blast radius of code changes by tracing all dependents
• Incremental indexing — Merkle tree change detection with file system watcher for real-time updates. Smart event filtering skips metadata-only changes (chmod, xattr)
• 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
• Embedding model — Optional local embedding via Candle (feature-gated embed-model). Context reordered to prioritize structural relations over code for better embedding quality
• Self-healing — Automatic SQLite corruption recovery with rebuild. Startup repair for incomplete indexing (Phase 3 failures)
• MCP protocol — JSON-RPC 2.0 over stdio, plug-and-play with Claude Code, Cursor, Windsurf, and other MCP clients
• Claude Code Plugin — First-class plugin with slash commands (/understand, /trace, /impact), agents, skills, auto-indexing hooks, StatusLine integration, and self-updating

Why code-graph-mcp?

Unlike 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.

Incremental by Design

BLAKE3 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.

Hybrid Search, Not Just Grep

Combines 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.

Scope-Aware Relation Extraction

The 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.

HTTP Request Flow Tracing

Unique 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.

Zero External Dependencies at Runtime

Single 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.

Built for AI Assistants

Every 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.

Performance

| Metric | Value | |--------|-------| | Indexing speed | 300+ files/second (single-threaded, release build) | | Incremental re-index | <250ms no-change detection via BLAKE3 Merkle tree | | FTS search P50 / P99 | <300us / <1ms | | Database overhead | ~3.5MB per 800 nodes | | Token savings | 5-20x fewer tokens per code understanding task vs grep+read |

Run code-graph-mcp benchmark on your own project to measure.

Efficiency: code-graph vs Traditional Tools

Real-world benchmarks comparing code-graph-mcp tools against traditional approaches (Grep + Read + Glob) on a 33-file Rust project (~537 AST nodes).

Tool Call Reduction

| Scenario | Traditional | code-graph | Savings | |----------|:-----------:|:----------:|:-------:| | Project architecture overview | 5-8 calls | 1 call (project_map) | ~85% | | Find function by concept | 3-5 calls | 1 call (semantic_code_search) | ~75% | | Trace 2-level call chain | 8-15 calls | 1 call (get_call_graph) | ~90% | | Pre-change impact analysis | 10-20+ calls | 1 call (impact_analysis) | ~95% | | Module structure & exports | 5+ calls | 1 call (module_overview) | ~80% | | File dependency mapping | 3-5 calls | 1 call (dependency_graph) | ~75% | | Similar code detection | N/A | 1 call (find_similar_code) | unique |

Overall Session Efficiency

| Metric | Without code-graph | With code-graph | Improvement | |--------|:------------------:|:---------------:|:-----------:| | Tool calls per navigation task | ~6 | ~1.2 | ~80% fewer | | Source lines read into context | ~8,000 lines | ~400 lines (structured) | ~95% less | | Navigation token cost | ~36K tokens | ~7K tokens | ~80% saved | | Full session token savings | — | — | 40-60% |

What code-graph Uniquely Enables

• Impact analysis — "Changing conn affects 33 functions across 4 files, 78 tests at HIGH risk" — impossible to derive manually with Grep
• Transitive call tracing — Follow main → run_serve → handle_message → handle_tools_call → conn in one query
• Semantic search — Find authenticate_session when searching "handle user login"
• Dependency strength — Not just "file A imports file B", but "file A uses 38 symbols from file B"

When Traditional Tools Are Still Better

| Use Case | Best Tool | |----------|-----------| | Exact string / constant search | Grep | | Reading a file to edit it | Read | | Finding files by name pattern | Glob |

Architecture

src/
├── domain.rs     # Shared constants, relation types, env-var config
├── mcp/          # MCP protocol layer (JSON-RPC, tool registry, server)
│   └── server/   # McpServer with IndexingState + CacheState sub-structs
├── parser/       # Tree-sitter parsing, relation extraction, LanguageConfig dispatch
├── indexer/      # 3-phase pipeline, Merkle tree, file watcher
├── storage/      # SQLite schema (v6), CRUD, FTS5, migrations
├── graph/        # Recursive CTE call graph queries
├── search/       # RRF fusion search combining BM25 + vector
├── embedding/    # Candle embedding model (optional, masked mean pooling)
├── sandbox/      # Context compressor with token estimation
└── utils/        # Language detection, config

Installation

Option 1: Claude Code Plugin (Recommended)

Install as a Claude Code plugin for the best experience — includes slash commands, agents, skills, auto-indexing hooks, StatusLine health display, and automatic updates:

# Step 1: Add the marketplace
/plugin marketplace add sdsrss/code-graph-mcp

# Step 2: Install the plugin
/plugin install code-graph-mcp

What you get:

• MCP Server — All code-graph tools available to Claude
• Slash Commands — /understand <module>, /trace <route>, /impact <symbol>
• Code Explorer Agent — Deep code understanding expert via code-explorer
• Auto-indexing Hook — Incremental index on every file edit (PostToolUse)
• StatusLine — Real-time health display (nodes, files, watch status) — compatible with other plugins' StatusLine via composite multiplexer
• Auto-update — Checks for new versions every 6h, updates silently

Manual Update

npm update -g @sdsrs/code-graph

Then reconnect the MCP server in Claude Code with /mcp.

Note: Auto-update is disabled in the source repo directory (dev mode). Use manual update when developing the plugin itself.

Invited-memory mode (quieter prompts)

By 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:

1. Adopt the plugin contract into your project's memory index (idempotent, self-heals):

   code-graph-mcp adopt

   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.
2. Set the activation env var in ~/.claude/settings.json:

   {
     "env": { "CODE_GRAPH_QUIET_HOOKS": "1" }
   }

3. 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.

Option 2: Claude Code MCP Server Only

Register as an MCP server without the plugin features:

claude mcp add code-graph-mcp -- npx -y @sdsrs/code-graph

Option 3: Cursor / Windsurf / Other MCP Clients

Add to your MCP settings file (e.g. ~/.cursor/mcp.json):

{
  "mcpServers": {
    "code-graph": {
      "command": "npx",
      "args": ["-y", "@sdsrs/code-graph"]
    }
  }
}

Option 4: npx (No Install)

Run directly without installing:

npx -y @sdsrs/code-graph

Option 5: npm (Global Install)

Install globally, then run anywhere:

npm install -g @sdsrs/code-graph
code-graph-mcp

Uninstallation

Claude Code Plugin

# Uninstall the plugin
/plugin uninstall code-graph-mcp

# (Optional) Remove the marketplace
/plugin marketplace remove code-graph-mcp

# (Optional) Clean up all config and cache data
node ~/.claude/plugins/cache/code-graph-mcp/code-graph-mcp/*/scripts/lifecycle.js uninstall

Claude Code MCP Server

claude mcp remove code-graph-mcp

Cursor / Windsurf / Other MCP Clients

Remove the code-graph entry from your MCP settings file (e.g. ~/.cursor/mcp.json).

npm (Global)

npm uninstall -g @sdsrs/code-graph

MCP Tools

| Tool | Description | |------|-------------| | project_map | Full project architecture: modules, dependencies, entry points, hot functions | | semantic_code_search | Hybrid BM25 + vector + graph search for AST nodes | | get_call_graph | Trace upstream/downstream call chains for a function | | trace_http_chain | Full request flow: route → handler → downstream call chain | | impact_analysis | Analyze the blast radius of changing a symbol | | module_overview | High-level overview of a module's structure and exports | | dependency_graph | Visualize dependency relationships between modules. Supports compact mode | | find_similar_code | Find semantically similar code via embeddings. Requires symbol_name or node_id | | get_ast_node | Extract a specific code symbol with signature, body, and relations. Supports compact mode | | ast_search | Search AST nodes by text and/or structural filters (type, return type, params) | | find_references | Find all references to a symbol (callers, importers, inheritors). Supports compact mode | | find_dead_code | Find unused code — orphan symbols and exported-but-unused public APIs |

CLI Commands

All tools are also available as CLI subcommands for shell scripts, hooks, and terminal workflows:

| Command | MCP Equivalent | Description | |---------|---------------|-------------| | search <query> | semantic_code_search | FTS5 search by concept | | ast-search [query] | ast_search | Structural search with --type/--returns/--params filters | | callgraph <symbol> | get_call_graph | Show call graph (callers/callees) | | impact <symbol> | impact_analysis | Impact analysis (callers, routes, risk level) | | show <symbol> | get_ast_node | Show symbol details (code, type, signature) | | map | project_map | Project architecture map | | overview <path> | module_overview | Module symbols grouped by file and type | | deps <file> | dependency_graph | File-level dependency graph | | trace <route> | trace_http_chain | Trace HTTP route → handler → downstream calls | | similar <symbol> | find_similar_code | Find semantically similar code (requires embeddings) | | refs <symbol> | find_references | Find all references to a symbol | | dead-code [path] | find_dead_code | Find unused code (orphans and exported-unused) | | grep <pattern> | — | AST-context grep (ripgrep + containing function/class) | | incremental-index | — | Run incremental index update (auto-creates DB if needed) | | health-check | get_index_status | Query index status and freshness | | benchmark | — | Benchmark index speed, query latency, token savings |

Common options: --json (JSON output), --compact (compact output), --limit N, --depth N, --file <path>.

Plugin Slash Commands

Available when installed as a Claude Code plugin:

| Command | Description | |---------|-------------| | /understand <module> | Deep dive into a module or file's architecture and relationships | | /trace <route> | Trace a full HTTP request flow from route to data layer | | /impact <symbol> | Analyze the impact scope of changing a symbol before modifying it | | /status | Show code-graph index status and embedding progress | | /rebuild | Force a full code-graph index rebuild |

Supported Languages (16)

| Language | Extensions | Relations Extracted | |----------|-----------|-------------------| | TypeScript | .ts, .tsx | calls, imports, exports, inherits, implements, routes_to | | JavaScript | .js, .jsx, .mjs, .cjs | calls, imports, exports, inherits, routes_to | | Go | .go | calls, imports, routes_to | | Python | .py, .pyi | calls, imports, inherits, routes_to | | Rust | .rs | calls, imports, inherits, implements | | Java | .java | calls, imports, inherits, implements | | C# | .cs | calls, imports, inherits, implements | | Kotlin | .kt, .kts | calls, imports, inherits | | Ruby | .rb | calls, imports, inherits | | PHP | .php | calls, imports, inherits, implements | | Swift | .swift | calls, imports, inherits | | Dart | .dart | calls, imports, implements | | C | .c, .h | calls, imports | | C++ | .cpp, .cc, .cxx, .hpp | calls, imports, inherits | | HTML | .html, .htm | structural parsing | | CSS | .css | structural parsing |

Storage

Uses SQLite with:

• FTS5 for full-text search
• sqlite-vec extension for vector similarity search
• Merkle tree hashes for incremental change detection

Data is stored in .code-graph/index.db under the project root (auto-created, gitignored).

Build from Source

Prerequisites

• Rust 1.75+ (2021 edition)
• A C compiler (for bundled SQLite / sqlite-vec)

Build

# Default build (with local embedding model)
cargo build --release

# Without embedding model (lighter build)
cargo build --release --no-default-features

Configure (from source)

Add the compiled binary to your MCP settings:

{
  "mcpServers": {
    "code-graph": {
      "command": "/path/to/target/release/code-graph-mcp"
    }
  }
}

Development

# Run tests
cargo test

# Run tests without embedding model
cargo test --no-default-features

# Check compilation
cargo check

# Run performance benchmarks (indexing, search, call graph)
cargo bench --no-default-features

License

See LICENSE for details.