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 across tiers of depth:
  • Full (calls + imports + inheritance): TypeScript/TSX, JavaScript, Go, Python, Rust, Java. HTTP route extraction additionally covers TypeScript/TSX + JavaScript (Express/Connect), Go (net/http), Python (Flask/FastAPI), and Rust axum (.route() chains with inline .nest() prefixes; named handlers only) — actix/rocket and Java Spring are not yet route-extracted
  • Smoke-tested (calls + imports + inheritance): C#, Kotlin, Ruby, PHP, Swift, Dart
  • Limited (functions + calls + #include imports + gtest test markers + C++ base-class inheritance + Class::method scope qualification): C, C++
  • Scripting: Bash (functions + commands + source/. imports), Markdown (headings)
  • File-FTS only (no AST symbol extraction): HTML, CSS, JSON
  • Test markers — detected from the AST for Rust (#[test] / #[cfg(test)]), JavaScript/TypeScript/TSX (describe/it/test blocks and their callbacks) and C/C++ (gtest TEST macros). Go, Python, Java and the rest fall back to path/name heuristics (tests/, src/test/java/, *_test.*, *.test.js, test_*, *Test)
  • Value/type references — a references relation for symbols that are used without being called, imported or inherited (path-qualified constants, type-position uses, functions passed as values): Rust, TypeScript/TSX, JavaScript, Python, Go, Java, C, C++
• 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, Rust axum)
• 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 (ESM export and CommonJS module.exports = { … } / exports.name = …), value/type references, 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/Connect, Flask/FastAPI, Go net/http, and Rust axum.

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 (get_ast_node + include_impact)	~95%
Module structure & exports	5+ calls	1 call (module_overview)	~80%
File dependency mapping	3-5 calls	1 call (module_overview + include_deps)	~75%
Similar code detection	N/A	1 call (get_ast_node + include_similar)	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.

Turning auto-update off

Environment variable	Effect
CODE_GRAPH_NO_AUTO_UPDATE=1	Skips the update check entirely — no version check, no download, and no updater process is started. A missing binary is still installed on first run, so the MCP server can't be left with no engine. Update manually with the command above.

Set it in the env block of ~/.claude/settings.json (the environment of the process hosting the MCP server), then reconnect with /mcp.

An update that keeps failing also stops hammering: after 5 failed attempts at the same release the updater drops to one retry per day (and retries immediately when a newer release is published), instead of re-downloading on every session. While it is in that state the statusline shows ⚠ update stuck and code-graph-mcp doctor prints the manual update command.

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 (idempotent, self-heals):

   code-graph-mcp adopt

   This writes a sentinel-wrapped managed block into <cwd>/CLAUDE.md (auto-loaded each session) plus <cwd>/.claude/plugin_code_graph_mcp.md (the full decision table, opened on demand). Run code-graph-mcp unadopt to remove both; content outside the managed block is kept.
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)

Run the teardown first, while the CLI still exists — npm 7 removed the preuninstall/postuninstall lifecycle scripts, so nothing runs on your behalf during npm uninstall. Doing it in the other order leaves the hook entries in ~/.claude/settings.json and the ~40 MB binary cache behind, with no command left on disk to remove them.

code-graph-mcp uninstall     # restore statusline, strip hooks, drop the cache
npm uninstall -g @sdsrs/code-graph

MCP Tools

tools/list advertises exactly these seven. Several older niche tools were folded into flags on them, so one call now covers what used to take a separate tool:

Tool	Description
project_map	Full project architecture: modules, dependencies, entry points, hot functions. include_centrality adds architectural chokepoints
semantic_code_search	Hybrid BM25 + vector search (RRF) for AST nodes. Supports compact mode
get_call_graph	Trace upstream/downstream call chains for a function. Pass route_path='GET /api/x' to trace an HTTP route → handler → downstream instead
get_ast_node	One symbol with signature, body and relations. include_impact adds the blast radius, include_similar embedding-similar nodes, include_references callers/callees. Supports compact mode
module_overview	Symbols in a directory or file, grouped by type and caller count. include_dead lists unreferenced symbols under the path; include_deps adds the file dependency graph (single-file paths only)
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, implementors, value/type references). Supports compact mode

Hidden aliases. These names are not in tools/list but still dispatch via tools/call, so existing clients keep working: trace_http_chain / find_http_route (→ get_call_graph with route_path), read_snippet (→ get_ast_node), dependency_graph, find_similar_code, find_dead_code, plus the management tools start_watch, stop_watch, get_index_status and rebuild_index. impact_analysis is removed — calling it returns Unknown tool; use get_ast_node with include_impact=true, or the CLI's impact --json for the full report.

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>	get_ast_node (include_impact=true)	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>	module_overview (include_deps=true)	File-level dependency graph
trace <route>	get_call_graph (route_path=…)	Trace HTTP route → handler → downstream calls
similar <symbol>	get_ast_node (include_similar=true)	Find semantically similar code (requires embeddings)
refs <symbol>	find_references	Find all references to a symbol
dead-code [path]	module_overview (include_dead=true)	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>.

As of v0.37.0 the CLI is clap-based: every subcommand has --help for its full flag list (code-graph-mcp <command> --help), value flags accept both --flag value and --flag=value, and unknown flags or malformed arguments fail fast with a clear error and a non-zero exit code (2) instead of being silently ignored. For example, trace hides downstream middleware with --no-middleware (shown by default), and snapshot is a create/inspect subcommand pair.

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 (19)

Language	Extensions	Relations Extracted
TypeScript	.ts, .tsx	calls, imports, exports, inherits, implements, routes_to, references
JavaScript	.js, .jsx, .mjs, .cjs	calls, imports, exports (ESM + CommonJS), inherits, routes_to, references
Go	.go	calls, imports, inherits, routes_to, references
Python	.py, .pyi	calls, imports, inherits, routes_to, references
Rust	.rs	calls, imports, implements, routes_to (axum), references
Java	.java	calls, imports, inherits, implements, references
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, inherits, implements
C	.c, .h	calls, imports, references
C++	.cpp, .cc, .cxx, .hpp, .hh, .hxx	calls, imports, inherits, references
Bash	.sh, .bash	functions, commands, source/. imports
Markdown	.md, .mdx, .markdown	headings
HTML	.html, .htm	file-FTS only (no AST symbols)
CSS	.css	file-FTS only (no AST symbols)
JSON	.json	file-FTS only (no AST symbols)

Known limitations:

• Rust has no inherits edges — the language has no class inheritance, so impl Trait for Type is recorded as implements and an inherits-filtered query returns empty for Rust.
• Kotlin/Swift interface conformance is recorded as inherits (both use a single : Type grammar for base classes and protocols/interfaces), so implements-filtered queries return empty for these two languages.
• Cross-file dead-code detection may false-positive a type whose only cross-file reference sits beyond the 4096-byte stored-content cap per node (documented accepted limitation, v0.97.1).

Team-shared graph snapshot

Skip the full local index for team members and CI runners by publishing a ~3-5MB graph snapshot with each GitHub release.

Setup (one-time):

1. Copy node_modules/code-graph-mcp/templates/code-graph-snapshot.yml into your repo's .github/workflows/.
2. Push a release tag. The workflow uploads code-graph-snapshot-<sha>.db.zst as a release asset.

Verify:

npx code-graph-mcp snapshot inspect ./code-graph-snapshot-<sha>.db.zst

After setup, the auto-fetch is opt-in per consumer: an untrusted repo could otherwise seed a misleading graph, so an unconfigured clone prints a hint and skips the install. Enable it with one of the trust signals below. These live in the environment (never in .code-graph.toml) so a committed/PR-injected config file cannot set them.

Environment variable	Effect
CODE_GRAPH_SNAPSHOT_TRUST_ORIGIN=1	Trust the auto-detected GitHub-release snapshot for this repo's origin remote, allowing auto-install.
CODE_GRAPH_SNAPSHOT_PIN=<blake3 hex>	Pin the expected artifact digest (64-char blake3 hex). When set it is the sole integrity authority — the download must match it, no network sidecar is consulted — and it also implicitly trusts the origin path.
CODE_GRAPH_SNAPSHOT_TRUST_URL=1	Honor a .code-graph.toml [snapshot] url override (an arbitrary, non-origin URL). Off by default because a committed URL could redirect the graph to an attacker-chosen database.

Integrity fail-closes: with no pin set and no fetchable <url>.blake3 sidecar, install is refused rather than accepting unverified content. Set a pin, or have the publisher serve the .blake3 sidecar alongside the snapshot. (file:// sources, used in tests, are exempt.)

Offline / air-gapped usage

The optional embedding model (needed for vector semantic search) is downloaded lazily on first use. To control that in a restricted environment:

Environment variable	Effect
CODE_GRAPH_MODEL_DIR=<dir>	Load model.safetensors from <dir> instead of downloading (highest-priority lookup). If the file isn't there, it warns and falls back to the normal search paths.
CODE_GRAPH_DISABLE_MODEL_DOWNLOAD=1	Disable the automatic background model download. An already-cached model is still loaded and used; the server otherwise stays in FTS5-only mode.

Installing the model by hand

CODE_GRAPH_MODEL_DIR is the supported manual route. Hand-populating the default cache dir (<platform cache>/code-graph/models) does not work: that dir is only trusted once extract_and_promote has written a .model-id marker, so a manually filled copy is treated as not-current and re-downloaded.

# Download + verify against the published checksum, then extract flat
# (the archive has no wrapping folder: model.safetensors, tokenizer.json, config.json).
curl -sL -o models.tar.gz \
  https://github.com/sdsrss/code-graph-mcp/releases/download/v<version>/models.tar.gz
curl -sL https://github.com/sdsrss/code-graph-mcp/releases/download/v<version>/models.tar.gz.sha256
sha256sum -c models.tar.gz.sha256
mkdir -p ~/.cache/code-graph/models-manual
tar -xzf models.tar.gz -C ~/.cache/code-graph/models-manual
export CODE_GRAPH_MODEL_DIR=~/.cache/code-graph/models-manual

On Windows use %LOCALAPPDATA%\code-graph\models-manual, and give tar a POSIX path for -C (/c/Users/<you>/...) — tar -C C:\... fails with "Cannot connect to C: resolve failed". The model is pinned by content hash, so a manual install must be redone on each version bump.

Diagnosing a model that never downloads

code-graph-mcp doctor reports the last download outcome, distinguishing "no download has been attempted" from "download FAILED after N attempt(s): …" with the underlying error. The raw record is <platform cache>/code-graph/model-download.json. On a network that performs TLS inspection, the download retries automatically against the OS certificate store after the bundled roots are rejected.

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 — FTS5-only (~10 MB binary, no embedding model)
cargo build --release

# With local embedding model (~150 MB binary; downloads ~120 MB model lazily on first semantic search)
cargo build --release --features embed-model

Direct cargo install users get the FTS5-only build by default. npm/npx/plugin users get the full hybrid (FTS5 + vector) build automatically — release CI compiles with --features embed-model for shipped binaries.

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.