codegraph

Give your AI the map before it starts exploring.

The Problem · What It Does · Quick Start · Commands · Languages · AI Integration · How It Works · Practices · Roadmap

The Problem

Large codebases are opaque. The structure lives in people's heads, not in tools.

A developer inherits a project and spends days grepping to understand what calls what. An AI agent burns half its token budget on grep, find, cat — re-discovering the same structure every session. An architect draws boundary rules on a whiteboard that erode within weeks because nothing enforces them. A CI pipeline catches test failures but can't tell you "this change silently affects 14 callers across 9 files."

The information exists — it's in the code itself. But without a structured map, everyone is navigating blind: developers guess, AI agents hallucinate, and architecture degrades one unreviewed change at a time.

What Codegraph Does

Codegraph builds a function-level dependency graph of your entire codebase — every function, every caller, every dependency — and keeps it current with sub-second incremental rebuilds.

It parses your code with tree-sitter (native Rust or WASM), stores the graph in SQLite, and gives you multiple ways to consume it:

CLI — developers explore, query, and audit their code from the terminal
MCP server — AI agents query the graph directly through 30 tools
CI gates — check and manifesto commands enforce quality thresholds with exit codes
Programmatic API — embed codegraph in your own tools via npm install

Instead of 30 tool calls to maybe discover half your dependencies, you get "this function has 14 callers across 9 files" instantly. Instead of hoping architecture rules are followed, you enforce them. Instead of finding breakage in production, diff-impact --staged catches it before you commit.

Free. Open source. Fully local. Zero network calls, zero telemetry. Your code stays on your machine. When you want deeper intelligence, bring your own LLM provider — your code only goes where you choose to send it.

Three commands to get started:

npm install -g @optave/codegraph
cd your-project
codegraph build

That's it. No config files, no Docker, no JVM, no API keys, no accounts. The graph is ready to query.

Why it matters

	Without codegraph	With codegraph
AI agents	Spend 20+ tool calls per session re-discovering code structure	Get full dependency context in one MCP call
AI agents	Modify `parseConfig()` without knowing 9 files import it	`fn-impact parseConfig` shows every caller before the edit
Developers	Inherit a codebase and grep for hours to understand what calls what	`context handleAuth -T` gives source, deps, callers, and tests in one command
Developers	Rename a function, break 14 call sites silently	`diff-impact --staged` catches breakage before you commit
CI pipelines	Catch test failures but miss structural degradation	`check --staged` fails the build when blast radius or complexity thresholds are exceeded
Architects	Draw boundary rules that erode within weeks	`manifesto` and `boundaries` enforce architecture rules on every commit

Feature comparison

_{Comparison last verified: March 2026. Full analysis: COMPETITIVE_ANALYSIS.md}

Capability	codegraph	joern	narsil-mcp	code-graph-rag	cpg	GitNexus	CodeMCP	axon
Function-level analysis	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Multi-language	11	14	32	11	~10	12	12	3
Semantic search	Yes	—	Yes	Yes	—	Yes	—	Yes
Hybrid BM25 + semantic	Yes	—	—	—	—	Yes	—	Yes
CODEOWNERS integration	Yes	—	—	—	—	—	—	—
Architecture boundary rules	Yes	—	—	—	—	—	—	—
CI validation predicates	Yes	—	—	—	—	—	—	—
Composite audit command	Yes	—	—	—	—	—	—	—
Batch querying	Yes	—	—	—	—	—	—	—
Graph snapshots	Yes	—	—	—	—	—	—	—
MCP / AI agent support	Yes	—	Yes	Yes	Yes	Yes	Yes	Yes
Git diff impact	Yes	—	—	—	—	Yes	Yes	Yes
Branch structural diff	Yes	—	—	—	—	—	—	Yes
Git co-change analysis	Yes	—	—	—	—	—	—	Yes
Watch mode	Yes	—	Yes	Yes	—	—	Yes	Yes
Dead code / role classification	Yes	—	Yes	—	—	—	Yes	Yes
Cycle detection	Yes	—	—	—	—	—	—	—
Incremental rebuilds	O(changed)	—	O(n) Merkle	—	—	—	Go only	Yes
Zero config	Yes	—	Yes	—	—	Yes	—	Yes
Embeddable JS library (`npm install`)	Yes	—	—	—	—	—	—	—
LLM-optional (works without API keys)	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
Dataflow analysis	Yes	Yes	—	—	Yes	—	—	—
Control flow graph (CFG)	Yes	Yes	—	—	Yes	—	—	—
AST node querying	Yes	Yes	—	—	Yes	—	—	—
Expanded node/edge types	Yes	Yes	—	—	Yes	—	—	—
GraphML / Neo4j export	Yes	Yes	—	—	—	—	—	—
Interactive graph viewer	Yes	—	—	—	—	—	—	—
Commercial use allowed	Yes	Yes	Yes	Yes	Yes	No	Paid	Yes
Open source	Yes	Yes	Yes	Yes	Yes	No	No	Yes

What makes codegraph different

	Differentiator	In practice
⚡	Always-fresh graph	Three-tier change detection: journal (O(changed)) → mtime+size (O(n) stats) → hash (O(changed) reads). Sub-second rebuilds even on large codebases
🔓	Zero-cost core, LLM-enhanced when you want	Full graph analysis with no API keys, no accounts, no cost. Optionally bring your own LLM provider — your code only goes where you choose
🔬	Function-level, not just files	Traces `handleAuth()` → `validateToken()` → `decryptJWT()` and shows 14 callers across 9 files break if `decryptJWT` changes
🏷️	Role classification	Every symbol auto-tagged as `entry`/`core`/`utility`/`adapter`/`dead`/`leaf` — agents instantly know what they're looking at
🤖	Built for AI agents	30-tool MCP server — AI assistants query your graph directly. Single-repo by default
🌐	Multi-language, one CLI	JS/TS + Python + Go + Rust + Java + C# + PHP + Ruby + HCL in a single graph
💥	Git diff impact	`codegraph diff-impact` shows changed functions, their callers, and full blast radius — enriched with historically coupled files from git co-change analysis. Ships with a GitHub Actions workflow
🧠	Hybrid search	BM25 keyword + semantic embeddings fused via RRF — `hybrid` (default), `semantic`, or `keyword` mode; multi-query via `"auth; token; JWT"`
🔬	Dataflow + CFG	Track how data flows through functions (`flows_to`, `returns`, `mutates`) and visualize intraprocedural control flow graphs for all 11 languages

🚀 Quick Start

# Install
npm install -g @optave/codegraph

# Build a graph for any project
cd your-project
codegraph build        # → .codegraph/graph.db created

# Start exploring
codegraph map          # see most-connected files
codegraph query myFunc # find any function, see callers & callees
codegraph deps src/index.ts  # file-level import/export map

Or install from source:

git clone https://github.com/optave/codegraph.git
cd codegraph && npm install && npm link

Dev builds: Pre-release tarballs are attached to GitHub Releases. Install with npm install -g <path-to-tarball>. Note that npm install -g <tarball-url> does not work because npm cannot resolve optional platform-specific dependencies from a URL — download the .tgz first, then install from the local file.

For AI agents

Add codegraph to your agent's instructions (e.g. CLAUDE.md):

Before modifying code, always:
1. `codegraph where <name>` — find where the symbol lives
2. `codegraph context <name> -T` — get full context (source, deps, callers)
3. `codegraph fn-impact <name> -T` — check blast radius before editing

After modifying code:
4. `codegraph diff-impact --staged -T` — verify impact before committing

Or connect directly via MCP:

codegraph mcp          # 30-tool MCP server — AI queries the graph directly

Full agent setup: AI Agent Guide · CLAUDE.md template

✨ Features

	Feature	Description
🔍	Symbol search	Find any function, class, or method by name — exact match priority, relevance scoring, `--file` and `--kind` filters
📁	File dependencies	See what a file imports and what imports it
💥	Impact analysis	Trace every file affected by a change (transitive)
🧬	Function-level tracing	Call chains, caller trees, function-level impact, and A→B pathfinding with qualified call resolution
🎯	Deep context	`context` gives AI agents source, deps, callers, signature, and tests for a function in one call; `audit --quick` gives structural summaries of files or functions
📍	Fast lookup	`where` shows exactly where a symbol is defined and used — minimal, fast
📊	Diff impact	Parse `git diff`, find overlapping functions, trace their callers
🔗	Co-change analysis	Analyze git history for files that always change together — surfaces hidden coupling the static graph can't see; enriches `diff-impact` with historically coupled files
🗺️	Module map	Bird's-eye view of your most-connected files
🏗️	Structure & hotspots	Directory cohesion scores, fan-in/fan-out hotspot detection, module boundaries
🏷️	Node role classification	Every symbol auto-tagged as `entry`/`core`/`utility`/`adapter`/`dead`/`leaf` based on connectivity patterns — agents instantly know architectural role
🔄	Cycle detection	Find circular dependencies at file or function level
📤	Export	DOT, Mermaid, JSON, GraphML, GraphSON, and Neo4j CSV graph export
🧠	Semantic search	Embeddings-powered natural language search with multi-query RRF ranking
👀	Watch mode	Incrementally update the graph as files change
🤖	MCP server	30-tool MCP server for AI assistants; single-repo by default, opt-in multi-repo
⚡	Always fresh	Three-tier incremental detection — sub-second rebuilds even on large codebases
🔬	Data flow analysis	Intraprocedural parameter tracking, return consumers, argument flows, and mutation detection — all 11 languages
🧮	Complexity metrics	Cognitive, cyclomatic, nesting depth, Halstead, and Maintainability Index per function
🏘️	Community detection	Louvain clustering to discover natural module boundaries and architectural drift
📜	Manifesto rule engine	Configurable pass/fail rules with warn/fail thresholds for CI gates via `check` (exit code 1 on fail)
👥	CODEOWNERS integration	Map graph nodes to CODEOWNERS entries — see who owns each function, ownership boundaries in `diff-impact`
💾	Graph snapshots	`snapshot save`/`restore` for instant DB backup and rollback — checkpoint before refactoring, restore without rebuilding
🔎	Hybrid BM25 + semantic search	FTS5 keyword search + embedding-based semantic search fused via Reciprocal Rank Fusion — `hybrid`, `semantic`, or `keyword` modes
📄	Pagination & NDJSON streaming	Universal `--limit`/`--offset` pagination on all MCP tools and CLI commands; `--ndjson` for newline-delimited JSON streaming
🔀	Branch structural diff	Compare code structure between two git refs — added/removed/changed symbols with transitive caller impact
🛡️	Architecture boundaries	User-defined dependency rules between modules with onion architecture preset — violations flagged in manifesto and CI
✅	CI validation predicates	`check` command with configurable gates: complexity, blast radius, cycles, boundary violations — exit code 0/1 for CI
📋	Composite audit	Single `audit` command combining explain + impact + health metrics per function — one call instead of 3-4
🚦	Triage queue	`triage` merges connectivity, hotspots, roles, and complexity into a ranked audit priority queue
📦	Batch querying	Accept a list of targets and return all results in one JSON payload — enables multi-agent parallel dispatch
🔬	Dataflow analysis	Track how data moves through functions with `flows_to`, `returns`, and `mutates` edges — all 11 languages, included by default, skip with `--no-dataflow`
🧩	Control flow graph	Intraprocedural CFG construction for all 11 languages — `cfg` command with text/DOT/Mermaid output, included by default, skip with `--no-cfg`
🔎	AST node querying	Stored queryable AST nodes (calls, `new`, string, regex, throw, await) — `ast` command with SQL GLOB pattern matching
🧬	Expanded node/edge types	`parameter`, `property`, `constant` node kinds with `parent_id` for sub-declaration queries; `contains`, `parameter_of`, `receiver` edge kinds
📊	Exports analysis	`exports <file>` shows all exported symbols with per-symbol consumers, re-export detection, and counts
📈	Interactive viewer	`codegraph plot` generates an interactive HTML graph viewer with hierarchical/force/radial layouts, complexity overlays, and drill-down
🏷️	Stable JSON schema	`normalizeSymbol` utility ensures consistent 7-field output (name, kind, file, line, endLine, role, fileHash) across all commands

See docs/examples for real-world CLI and MCP usage examples.

📦 Commands

Build & Watch

codegraph build [dir]          # Parse and build the dependency graph
codegraph build --no-incremental  # Force full rebuild
codegraph build --dataflow     # Extract data flow edges (flows_to, returns, mutates)
codegraph build --engine wasm  # Force WASM engine (skip native)
codegraph watch [dir]          # Watch for changes, update graph incrementally

Query & Explore

codegraph query <name>         # Find a symbol — shows callers and callees
codegraph deps <file>          # File imports/exports
codegraph map                  # Top 20 most-connected files
codegraph map -n 50 --no-tests # Top 50, excluding test files
codegraph where <name>         # Where is a symbol defined and used?
codegraph where --file src/db.js  # List symbols, imports, exports for a file
codegraph stats                # Graph health: nodes, edges, languages, quality score
codegraph roles                # Node role classification (entry, core, utility, adapter, dead, leaf)
codegraph roles --role dead -T # Find dead code (unreferenced, non-exported symbols)
codegraph roles --role core --file src/  # Core symbols in src/
codegraph exports src/queries.js  # Per-symbol consumer analysis (who calls each export)
codegraph children <name>         # List parameters, properties, constants of a symbol

Deep Context (AI-Optimized)

codegraph context <name>       # Full context: source, deps, callers, signature, tests
codegraph context <name> --depth 2 --no-tests  # Include callee source 2 levels deep
codegraph audit <file> --quick    # Structural summary: public API, internals, data flow
codegraph audit <function> --quick  # Function summary: signature, calls, callers, tests

Impact Analysis

codegraph impact <file>        # Transitive reverse dependency trace
codegraph query <name>         # Function-level: callers, callees, call chain
codegraph query <name> --no-tests --depth 5
codegraph fn-impact <name>     # What functions break if this one changes
codegraph path <from> <to>            # Shortest path between two symbols (A calls...calls B)
codegraph path <from> <to> --reverse  # Follow edges backward
codegraph path <from> <to> --depth 5 --kinds calls,imports
codegraph diff-impact          # Impact of unstaged git changes
codegraph diff-impact --staged # Impact of staged changes
codegraph diff-impact HEAD~3   # Impact vs a specific ref
codegraph diff-impact main --format mermaid -T  # Mermaid flowchart of blast radius
codegraph branch-compare main feature-branch    # Structural diff between two refs
codegraph branch-compare main HEAD --no-tests   # Symbols added/removed/changed vs main
codegraph branch-compare v2.4.0 v2.5.0 --json   # JSON output for programmatic use
codegraph branch-compare main HEAD --format mermaid  # Mermaid diagram of structural changes

Co-Change Analysis

Analyze git history to find files that always change together — surfaces hidden coupling the static graph can't see. Requires a git repository.

codegraph co-change --analyze          # Scan git history and populate co-change data
codegraph co-change src/queries.js     # Show co-change partners for a file
codegraph co-change                    # Show top co-changing file pairs globally
codegraph co-change --since 6m         # Limit to last 6 months of history
codegraph co-change --min-jaccard 0.5  # Only show strong coupling (Jaccard >= 0.5)
codegraph co-change --min-support 5    # Minimum co-commit count
codegraph co-change --full             # Include all details

Co-change data also enriches diff-impact — historically coupled files appear in a historicallyCoupled section alongside the static dependency analysis.

Structure & Hotspots

codegraph structure            # Directory overview with cohesion scores
codegraph triage --level file  # Files with extreme fan-in, fan-out, or density
codegraph triage --level directory --sort coupling --no-tests

Code Health & Architecture

codegraph complexity              # Per-function cognitive, cyclomatic, nesting, MI
codegraph complexity --health -T  # Full Halstead health view (volume, effort, bugs, MI)
codegraph complexity --sort mi -T # Sort by worst maintainability index
codegraph complexity --above-threshold -T  # Only functions exceeding warn thresholds
codegraph communities             # Louvain community detection — natural module boundaries
codegraph communities --drift -T  # Drift analysis only — split/merge candidates
codegraph communities --functions # Function-level community detection
codegraph check                   # Pass/fail rule engine (exit code 1 on fail)
codegraph check -T                # Exclude test files from rule evaluation

Dataflow, CFG & AST

codegraph dataflow <name>             # Data flow edges for a function (flows_to, returns, mutates)
codegraph dataflow <name> --impact    # Transitive data-dependent blast radius
codegraph cfg <name>                  # Control flow graph (text format)
codegraph cfg <name> --format dot     # CFG as Graphviz DOT
codegraph cfg <name> --format mermaid # CFG as Mermaid diagram
codegraph ast                         # List all stored AST nodes
codegraph ast "handleAuth"            # Search AST nodes by pattern (GLOB)
codegraph ast -k call                 # Filter by kind: call, new, string, regex, throw, await
codegraph ast -k throw --file src/    # Combine kind and file filters

Note: Dataflow and CFG are included by default for all 11 languages. Use --no-dataflow / --no-cfg for faster builds.

Audit, Triage & Batch

Composite commands for risk-driven workflows and multi-agent dispatch.

codegraph audit <file-or-function>    # Combined structural summary + impact + health in one report
codegraph audit <target> --quick      # Structural summary only (skip impact and health)
codegraph audit src/queries.js -T     # Audit all functions in a file
codegraph triage                      # Ranked audit priority queue (connectivity + hotspots + roles)
codegraph triage -T --limit 20        # Top 20 riskiest functions, excluding tests
codegraph triage --level file -T      # File-level hotspot analysis
codegraph triage --level directory -T # Directory-level hotspot analysis
codegraph batch target1 target2 ...   # Batch query multiple targets in one call
codegraph batch --json targets.json   # Batch from a JSON file

CI Validation

codegraph check provides configurable pass/fail predicates for CI gates and state machines. Exit code 0 = pass, 1 = fail.

codegraph check                             # Run manifesto rules on whole codebase
codegraph check --staged                    # Check staged changes (diff predicates)
codegraph check --staged --rules            # Run both diff predicates AND manifesto rules
codegraph check --no-new-cycles             # Fail if staged changes introduce cycles
codegraph check --max-complexity 30         # Fail if any function exceeds complexity threshold
codegraph check --max-blast-radius 50       # Fail if blast radius exceeds limit
codegraph check --no-boundary-violations    # Fail on architecture boundary violations
codegraph check main                        # Check current branch vs main

CODEOWNERS

Map graph symbols to CODEOWNERS entries. Shows who owns each function and surfaces ownership boundaries.

codegraph owners                   # Show ownership for all symbols
codegraph owners src/queries.js    # Ownership for symbols in a specific file
codegraph owners --boundary        # Show ownership boundaries between modules
codegraph owners --owner @backend  # Filter by owner

Ownership data also enriches diff-impact — affected owners and suggested reviewers appear alongside the static dependency analysis.

Snapshots

Lightweight SQLite DB backup and restore — checkpoint before refactoring, instantly rollback without rebuilding.

codegraph snapshot save before-refactor   # Save a named snapshot
codegraph snapshot list                   # List all snapshots
codegraph snapshot restore before-refactor  # Restore a snapshot
codegraph snapshot delete before-refactor   # Delete a snapshot

Export & Visualization

codegraph export -f dot        # Graphviz DOT format
codegraph export -f mermaid    # Mermaid diagram
codegraph export -f json       # JSON graph
codegraph export -f graphml    # GraphML (XML standard)
codegraph export -f graphson   # GraphSON (TinkerPop v3 / Gremlin)
codegraph export -f neo4j      # Neo4j CSV (bulk import, separate nodes/relationships files)
codegraph export --functions -o graph.dot  # Function-level, write to file
codegraph plot                 # Interactive HTML viewer with force/hierarchical/radial layouts
codegraph cycles               # Detect circular dependencies
codegraph cycles --functions   # Function-level cycles

Semantic Search

Local embeddings for every function, method, and class — search by natural language. Everything runs locally using @huggingface/transformers — no API keys needed.

codegraph embed                # Build embeddings (default: nomic-v1.5)
codegraph embed --model nomic  # Use a different model
codegraph search "handle authentication"
codegraph search "parse config" --min-score 0.4 -n 10
codegraph search "parseConfig" --mode keyword   # BM25 keyword-only (exact names)
codegraph search "auth flow" --mode semantic    # Embedding-only (conceptual)
codegraph search "auth flow" --mode hybrid      # BM25 + semantic RRF fusion (default)
codegraph models               # List available models

Multi-query search

Separate queries with ; to search from multiple angles at once. Results are ranked using Reciprocal Rank Fusion (RRF) — items that rank highly across multiple queries rise to the top.

codegraph search "auth middleware; JWT validation"
codegraph search "parse config; read settings; load env" -n 20
codegraph search "error handling; retry logic" --kind function
codegraph search "database connection; query builder" --rrf-k 30

A single trailing semicolon is ignored (falls back to single-query mode). The --rrf-k flag controls the RRF smoothing constant (default 60) — lower values give more weight to top-ranked results.

Available Models

Flag	Model	Dimensions	Size	License	Notes
`minilm`	all-MiniLM-L6-v2	384	~23 MB	Apache-2.0	Fastest, good for quick iteration
`jina-small`	jina-embeddings-v2-small-en	512	~33 MB	Apache-2.0	Better quality, still small
`jina-base`	jina-embeddings-v2-base-en	768	~137 MB	Apache-2.0	High quality, 8192 token context
`jina-code`	jina-embeddings-v2-base-code	768	~137 MB	Apache-2.0	Best for code search, trained on code+text (requires HF token)
`nomic`	nomic-embed-text-v1	768	~137 MB	Apache-2.0	Good quality, 8192 context
`nomic-v1.5` (default)	nomic-embed-text-v1.5	768	~137 MB	Apache-2.0	Improved nomic, Matryoshka dimensions
`bge-large`	bge-large-en-v1.5	1024	~335 MB	MIT	Best general retrieval, top MTEB scores

The model used during embed is stored in the database, so search auto-detects it — no need to pass --model when searching.

Multi-Repo Registry

Manage a global registry of codegraph-enabled projects. The registry stores paths to your built graphs so the MCP server can query them when multi-repo mode is enabled.

codegraph registry list        # List all registered repos
codegraph registry list --json # JSON output
codegraph registry add <dir>   # Register a project directory
codegraph registry add <dir> -n my-name  # Custom name
codegraph registry remove <name>  # Unregister

codegraph build auto-registers the project — no manual setup needed.

Common Flags

Flag	Description
`-d, --db <path>`	Custom path to `graph.db`
`-T, --no-tests`	Exclude `.test.`, `.spec.`, `__test__` files (available on most query commands including `query`, `fn-impact`, `path`, `context`, `where`, `diff-impact`, `search`, `map`, `roles`, `co-change`, `deps`, `impact`, `complexity`, `communities`, `branch-compare`, `audit`, `triage`, `check`, `dataflow`, `cfg`, `ast`, `exports`, `children`)
`--depth <n>`	Transitive trace depth (default varies by command)
`-j, --json`	Output as JSON
`-v, --verbose`	Enable debug output
`--engine <engine>`	Parser engine: `native`, `wasm`, or `auto` (default: `auto`)
`-k, --kind <kind>`	Filter by kind: `function`, `method`, `class`, `interface`, `type`, `struct`, `enum`, `trait`, `record`, `module`, `parameter`, `property`, `constant`
`-f, --file <path>`	Scope to a specific file (`fn`, `context`, `where`)
`--mode <mode>`	Search mode: `hybrid` (default), `semantic`, or `keyword` (`search`)
`--ndjson`	Output as newline-delimited JSON (one object per line)
`--limit <n>`	Limit number of results
`--offset <n>`	Skip first N results (pagination)
`--rrf-k <n>`	RRF smoothing constant for multi-query search (default 60)

🌐 Language Support

Language	Extensions	Coverage
	`.js`, `.jsx`, `.mjs`, `.cjs`	Full — functions, classes, imports, call sites, dataflow
	`.ts`, `.tsx`	Full — interfaces, type aliases, `.d.ts`, dataflow
	`.py`	Functions, classes, methods, imports, decorators, dataflow
	`.go`	Functions, methods, structs, interfaces, imports, call sites, dataflow
	`.rs`	Functions, methods, structs, traits, `use` imports, call sites, dataflow
	`.java`	Classes, methods, constructors, interfaces, imports, call sites, dataflow
	`.cs`	Classes, structs, records, interfaces, enums, methods, constructors, using directives, invocations, dataflow
	`.php`	Functions, classes, interfaces, traits, enums, methods, namespace use, calls, dataflow
	`.rb`	Classes, modules, methods, singleton methods, require/require_relative, include/extend, dataflow
	`.tf`, `.hcl`	Resource, data, variable, module, output blocks

⚙️ How It Works

┌──────────┐    ┌───────────┐    ┌───────────┐    ┌──────────┐    ┌─────────┐
│  Source  │──▶│ tree-sitter│──▶│  Extract  │──▶│  Resolve │──▶│ SQLite  │
│  Files   │    │   Parse   │    │  Symbols  │    │  Imports │    │   DB    │
└──────────┘    └───────────┘    └───────────┘    └──────────┘    └─────────┘
                                                                       │
                                                                       ▼
                                                                 ┌─────────┐
                                                                 │  Query  │
                                                                 └─────────┘

Parse — tree-sitter parses every source file into an AST (native Rust engine or WASM fallback)
Extract — Functions, classes, methods, interfaces, imports, exports, call sites, parameters, properties, and constants are extracted
Resolve — Imports are resolved to actual files (handles ESM conventions, tsconfig.json path aliases, baseUrl)
Store — Everything goes into SQLite as nodes + edges with tree-sitter node boundaries, plus structural edges (contains, parameter_of, receiver)
Analyze (opt-in) — Complexity metrics, control flow graphs (--cfg), dataflow edges (--dataflow), and AST node storage
Query — All queries run locally against the SQLite DB — typically under 100ms

Incremental Rebuilds

The graph stays current without re-parsing your entire codebase. Three-tier change detection ensures rebuilds are proportional to what changed, not the size of the project:

Tier 0 — Journal (O(changed)): If codegraph watch was running, a change journal records exactly which files were touched. The next build reads the journal and only processes those files — zero filesystem scanning
Tier 1 — mtime+size (O(n) stats, O(changed) reads): No journal? Codegraph stats every file and compares mtime + size against stored values. Matching files are skipped without reading a single byte
Tier 2 — Hash (O(changed) reads): Files that fail the mtime/size check are read and MD5-hashed. Only files whose hash actually changed get re-parsed and re-inserted

Result: change one file in a 3,000-file project and the rebuild completes in under a second. Put it in a commit hook, a file watcher, or let your AI agent trigger it.

Dual Engine

Codegraph ships with two parsing engines:

Engine	How it works	When it's used
Native (Rust)	napi-rs addon built from `crates/codegraph-core/` — parallel multi-core parsing via rayon	Auto-selected when the prebuilt binary is available
WASM	`web-tree-sitter` with pre-built `.wasm` grammars in `grammars/`	Fallback when the native addon isn't installed

Both engines produce identical output. Use --engine native|wasm|auto to control selection (default: auto).

Call Resolution

Calls are resolved with qualified resolution — method calls (obj.method()) are distinguished from standalone function calls, and built-in receivers (console, Math, JSON, Array, Promise, etc.) are filtered out automatically. Import scope is respected: a call to foo() only resolves to functions that are actually imported or defined in the same file, eliminating false positives from name collisions.

Priority	Source	Confidence
1	Import-aware — `import { foo } from './bar'` → link to `bar`	`1.0`
2	Same-file — definitions in the current file	`1.0`
3	Same directory — definitions in sibling files (standalone calls only)	`0.7`
4	Same parent directory — definitions in sibling dirs (standalone calls only)	`0.5`
5	Method hierarchy — resolved through `extends`/`implements`	varies

Method calls on unknown receivers skip global fallback entirely — stmt.run() will never resolve to a standalone run function in another file. Duplicate caller/callee edges are deduplicated automatically. Dynamic patterns like fn.call(), fn.apply(), fn.bind(), and obj["method"]() are also detected on a best-effort basis.

Codegraph also extracts symbols from common callback patterns: Commander .command().action() callbacks (as command:build), Express route handlers (as route:GET /api/users), and event emitter listeners (as event:data).

📊 Performance

Self-measured on every release via CI (build benchmarks | embedding benchmarks):

Metric	Latest
Build speed (native)	12.3 ms/file
Build speed (WASM)	16.3 ms/file
Query time	3ms
No-op rebuild (native)	5ms
1-file rebuild (native)	375ms
Query: fn-deps	0.8ms
Query: path	0.8ms
~50,000 files (est.)	~615.0s build

Metrics are normalized per file for cross-version comparability. Times above are for a full initial build — incremental rebuilds only re-parse changed files.

Lightweight Footprint

Only 3 runtime dependencies — everything else is optional or a devDependency:

Dependency	What it does
better-sqlite3	Fast, synchronous SQLite driver
commander	CLI argument parsing
web-tree-sitter	WASM tree-sitter bindings

Optional: @huggingface/transformers (semantic search), @modelcontextprotocol/sdk (MCP server) — lazy-loaded only when needed.

🤖 AI Agent Integration

MCP Server

Codegraph includes a built-in Model Context Protocol server with 30 tools (31 in multi-repo mode), so AI assistants can query your dependency graph directly:

codegraph mcp                  # Single-repo mode (default) — only local project
codegraph mcp --multi-repo     # Enable access to all registered repos
codegraph mcp --repos a,b      # Restrict to specific repos (implies --multi-repo)

Single-repo mode (default): Tools operate only on the local .codegraph/graph.db. The repo parameter and list_repos tool are not exposed to the AI agent.

Multi-repo mode (--multi-repo): All tools gain an optional repo parameter to target any registered repository, and list_repos becomes available. Use --repos to restrict which repos the agent can access.

CLAUDE.md / Agent Instructions

Add this to your project's CLAUDE.md to help AI agents use codegraph (full template in the AI Agent Guide):

## Code Navigation

This project uses codegraph. The database is at `.codegraph/graph.db`.

### Before modifying code, always:
1. `codegraph where <name>` — find where the symbol lives
2. `codegraph audit <file-or-function> --quick` — understand the structure
3. `codegraph context <name> -T` — get full context (source, deps, callers)
4. `codegraph fn-impact <name> -T` — check blast radius before editing

### After modifying code:
5. `codegraph diff-impact --staged -T` — verify impact before committing

### Other useful commands
- `codegraph build .` — rebuild the graph (incremental by default)
- `codegraph map` — module overview
- `codegraph query <name> -T` — function call chain (callers + callees)
- `codegraph path <from> <to> -T` — shortest call path between two symbols
- `codegraph deps <file>` — file-level dependencies
- `codegraph roles --role dead -T` — find dead code (unreferenced symbols)
- `codegraph roles --role core -T` — find core symbols (high fan-in)
- `codegraph co-change <file>` — files that historically change together
- `codegraph complexity -T` — per-function complexity metrics (cognitive, cyclomatic, MI)
- `codegraph communities --drift -T` — module boundary drift analysis
- `codegraph check -T` — pass/fail rule check (CI gate, exit code 1 on fail)
- `codegraph audit <target> -T` — combined structural summary + impact + health in one report
- `codegraph triage -T` — ranked audit priority queue
- `codegraph triage --level file -T` — file-level hotspot analysis
- `codegraph check --staged` — CI validation predicates (exit code 0/1)
- `codegraph batch target1 target2` — batch query multiple targets at once
- `codegraph owners [target]` — CODEOWNERS mapping for symbols
- `codegraph snapshot save <name>` — checkpoint the graph DB before refactoring
- `codegraph branch-compare main HEAD -T` — structural diff between two refs (added/removed/changed symbols)
- `codegraph exports <file>` — per-symbol consumer analysis (who calls each export)
- `codegraph children <name>` — list parameters, properties, constants of a symbol
- `codegraph dataflow <name>` — data flow edges (flows_to, returns, mutates)
- `codegraph cfg <name>` — intraprocedural control flow graph
- `codegraph ast <pattern>` — search stored AST nodes (calls, new, string, regex, throw, await)
- `codegraph plot` — interactive HTML dependency graph viewer
- `codegraph search "<query>"` — hybrid search (requires `codegraph embed`)
- `codegraph search "<query>" --mode keyword` — BM25 keyword search
- `codegraph cycles` — check for circular dependencies

### Flags
- `-T` / `--no-tests` — exclude test files (use by default)
- `-j` / `--json` — JSON output for programmatic use
- `-f, --file <path>` — scope to a specific file
- `-k, --kind <kind>` — filter by symbol kind

### Semantic search

Use `codegraph search` to find functions by intent rather than exact name.
When a single query might miss results, combine multiple angles with `;`:

  codegraph search "validate auth; check token; verify JWT"
  codegraph search "parse config; load settings" --kind function

Multi-query search uses Reciprocal Rank Fusion — functions that rank
highly across several queries surface first. This is especially useful
when you're not sure what naming convention the codebase uses.

When writing multi-queries, use 2-4 sub-queries (2-4 words each) that
attack the problem from different angles. Pick from these strategies:
- **Naming variants**: cover synonyms the author might have used
  ("send email; notify user; deliver message")
- **Abstraction levels**: pair high-level intent with low-level operation
  ("handle payment; charge credit card")
- **Input/output sides**: cover the read half and write half
  ("parse config; apply settings")
- **Domain + technical**: bridge business language and implementation
  ("onboard tenant; create organization; provision workspace")

Use `--kind function` to cut noise. Use `--file <pattern>` to scope.

📋 Recommended Practices

See docs/guides/recommended-practices.md for integration guides:

Git hooks — auto-rebuild on commit, impact checks on push, commit message enrichment
CI/CD — PR impact comments, threshold gates, graph caching
AI agents — MCP server, CLAUDE.md templates, Claude Code hooks
Developer workflow — watch mode, explore-before-you-edit, semantic search
Secure credentials — apiKeyCommand with 1Password, Bitwarden, Vault, macOS Keychain, pass

For AI-specific integration, see the AI Agent Guide — a comprehensive reference covering the 6-step agent workflow, complete command-to-MCP mapping, Claude Code hooks, and token-saving patterns.

🔁 CI / GitHub Actions

Codegraph ships with a ready-to-use GitHub Actions workflow that comments impact analysis on every pull request.

Copy .github/workflows/codegraph-impact.yml to your repo, and every PR will get a comment like:

3 functions changed → 12 callers affected across 7 files

🛠️ Configuration

Create a .codegraphrc.json in your project root to customize behavior:

{
  "include": ["src/**", "lib/**"],
  "exclude": ["**/*.test.js", "**/__mocks__/**"],
  "ignoreDirs": ["node_modules", ".git", "dist"],
  "extensions": [".js", ".ts", ".tsx", ".py"],
  "aliases": {
    "@/": "./src/",
    "@utils/": "./src/utils/"
  },
  "build": {
    "incremental": true
  },
  "query": {
    "excludeTests": true
  }
}

Tip: excludeTests can also be set at the top level as a shorthand — { "excludeTests": true } is equivalent to nesting it under query. If both are present, the nested query.excludeTests takes precedence.

Manifesto rules

Configure pass/fail thresholds for codegraph check (manifesto mode):

{
  "manifesto": {
    "rules": {
      "cognitive_complexity": { "warn": 15, "fail": 30 },
      "cyclomatic_complexity": { "warn": 10, "fail": 20 },
      "nesting_depth": { "warn": 4, "fail": 6 },
      "maintainability_index": { "warn": 40, "fail": 20 },
      "halstead_bugs": { "warn": 0.5, "fail": 1.0 }
    }
  }
}

When any function exceeds a fail threshold, codegraph check exits with code 1 — perfect for CI gates.

LLM credentials

Codegraph supports an apiKeyCommand field for secure credential management. Instead of storing API keys in config files or environment variables, you can shell out to a secret manager at runtime:

{
  "llm": {
    "provider": "openai",
    "apiKeyCommand": "op read op://vault/openai/api-key"
  }
}

The command is split on whitespace and executed with execFileSync (no shell injection risk). Priority: command output > CODEGRAPH_LLM_API_KEY env var > file config. On failure, codegraph warns and falls back to the next source.

Works with any secret manager: 1Password CLI (op), Bitwarden (bw), pass, HashiCorp Vault, macOS Keychain (security), AWS Secrets Manager, etc.

📖 Programmatic API

Codegraph also exports a full API for use in your own tools:

import { buildGraph, queryNameData, findCycles, exportDOT, normalizeSymbol } from '@optave/codegraph';

// Build the graph
buildGraph('/path/to/project');

// Query programmatically
const results = queryNameData('myFunction', '/path/to/.codegraph/graph.db');
// All query results use normalizeSymbol for a stable 7-field schema

import { parseFileAuto, getActiveEngine, isNativeAvailable } from '@optave/codegraph';

// Check which engine is active
console.log(getActiveEngine());      // 'native' or 'wasm'
console.log(isNativeAvailable());    // true if Rust addon is installed

// Parse a single file (uses auto-selected engine)
const symbols = await parseFileAuto('/path/to/file.ts');

import { searchData, multiSearchData, buildEmbeddings } from '@optave/codegraph';

// Build embeddings (one-time)
await buildEmbeddings('/path/to/project');

// Single-query search
const { results } = await searchData('handle auth', dbPath);

// Multi-query search with RRF ranking
const { results: fused } = await multiSearchData(
  ['auth middleware', 'JWT validation'],
  dbPath,
  { limit: 10, minScore: 0.3 }
);
// Each result has: { name, kind, file, line, rrf, queryScores[] }

⚠️ Limitations

No full type inference — parses .d.ts interfaces but doesn't use TypeScript's type checker for overload resolution
Dynamic calls are best-effort — complex computed property access and eval patterns are not resolved
Python imports — resolves relative imports but doesn't follow sys.path or virtual environment packages
Dataflow analysis — intraprocedural (single-function scope), not interprocedural

🗺️ Roadmap

See ROADMAP.md for the full development roadmap and STABILITY.md for the stability policy and versioning guarantees. Current plan:

~~Rust Core~~ — Complete (v1.3.0) — native tree-sitter parsing via napi-rs, parallel multi-core parsing, incremental re-parsing, import resolution & cycle detection in Rust
~~Foundation Hardening~~ — Complete (v1.4.0) — parser registry, 12-tool MCP server with multi-repo support, test coverage 62%→75%, apiKeyCommand secret resolution, global repo registry
~~Deep Analysis~~ — Complete (v3.0.0) — dataflow analysis (flows_to, returns, mutates), intraprocedural CFG for all 11 languages, stored AST nodes, expanded node/edge types (parameter, property, constant, contains, parameter_of, receiver), GraphML/GraphSON/Neo4j CSV export, interactive HTML viewer, CLI consolidation, stable JSON schema
Architectural Refactoring — parser plugin system, repository pattern, pipeline builder, engine strategy, domain errors, curated API
Natural Language Queries — codegraph ask command, conversational sessions
Expanded Language Support — 8 new languages (12 → 20)
GitHub Integration & CI — reusable GitHub Action, PR review, SARIF output
TypeScript Migration — gradual migration from JS to TypeScript

🤝 Contributing

Contributions are welcome! See CONTRIBUTING.md for the full guide — setup, workflow, commit convention, testing, and architecture notes.

git clone https://github.com/optave/codegraph.git
cd codegraph
npm install
npm test

Looking to add a new language? Check out Adding a New Language.

📄 License

Apache-2.0

_{Built with tree-sitter and better-sqlite3. Your code stays on your machine.}

Name		Name	Last commit message	Last commit date
Latest commit History 553 Commits
.claude		.claude
.github		.github
.husky		.husky
crates/codegraph-core		crates/codegraph-core
docs		docs
generated		generated
scripts		scripts
src		src
tests		tests
.codegraphrc.example.json		.codegraphrc.example.json
.codegraphrc.json		.codegraphrc.json
.gitattributes		.gitattributes
.gitignore		.gitignore
.npmignore		.npmignore
.versionrc.json		.versionrc.json
CHANGELOG.md		CHANGELOG.md
CLA.md		CLA.md
CLAUDE.md		CLAUDE.md
CODE_OF_CONDUCT.md		CODE_OF_CONDUCT.md
CONTRIBUTING.md		CONTRIBUTING.md
Cargo.toml		Cargo.toml
FOUNDATION.md		FOUNDATION.md
LICENSE		LICENSE
README.md		README.md
SECURITY.md		SECURITY.md
STABILITY.md		STABILITY.md
SUPPORT.md		SUPPORT.md
biome.json		biome.json
commitlint.config.js		commitlint.config.js
package-lock.json		package-lock.json
package.json		package.json
vitest.config.js		vitest.config.js

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codegraph

The Problem

What Codegraph Does

Why it matters

Feature comparison

What makes codegraph different

🚀 Quick Start

For AI agents

✨ Features

📦 Commands

Build & Watch

Query & Explore

Deep Context (AI-Optimized)

Impact Analysis

Co-Change Analysis

Structure & Hotspots

Code Health & Architecture

Dataflow, CFG & AST

Audit, Triage & Batch

CI Validation

CODEOWNERS

Snapshots

Export & Visualization

Semantic Search

Multi-query search

Available Models

Multi-Repo Registry

Common Flags

🌐 Language Support

⚙️ How It Works

Incremental Rebuilds

Dual Engine

Call Resolution

📊 Performance

Lightweight Footprint

🤖 AI Agent Integration

MCP Server

CLAUDE.md / Agent Instructions

📋 Recommended Practices

🔁 CI / GitHub Actions

🛠️ Configuration

Manifesto rules

LLM credentials

📖 Programmatic API

⚠️ Limitations

🗺️ Roadmap

🤝 Contributing

📄 License

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