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

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The Problem

AI agents face an impossible trade-off. They either spend thousands of tokens reading files to understand a codebase's structure — blowing up their context window until quality degrades — or they assume how things work, and the assumptions are often wrong. Either way, things break. The larger the codebase, the worse it gets.

An agent modifies a function without knowing 9 files import it. It misreads what a helper does and builds logic on top of that misunderstanding. It leaves dead code behind after a refactor. The PR gets opened, and your reviewer — human or automated — flags the same structural issues again and again: "this breaks 14 callers," "that function already exists," "this export is now dead." If the reviewer catches it, that's multiple rounds of back-and-forth. If they don't, it can ship to production. Multiply that by every PR, every developer, every repo.

The information to prevent these issues exists — it's in the code itself. But without a structured map, agents lack the context to get it right consistently, reviewers waste cycles on preventable issues, 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 exposes it where it matters most:

• MCP server — AI agents query the graph directly through 30 tools — one call instead of 30 grep/find/cat invocations
• CLI — developers and agents explore, query, and audit code from the terminal
• 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 an agent editing code without structural context and letting reviewers catch the fallout, it knows "this function has 14 callers across 9 files" before it touches anything. Dead exports, circular dependencies, and boundary violations surface during development — not during review. The result: PRs that need fewer review rounds.

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 a queryable graph:

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

No config files, no Docker, no JVM, no API keys, no accounts. Point your agent at the MCP server and it has structural awareness of your codebase.

Why it matters

	Without codegraph	With codegraph
Code review	Reviewers flag broken callers, dead code, and boundary violations round after round	Structural issues are caught during development — PRs pass review with fewer rounds
AI agents	Modify parseConfig() without knowing 9 files import it — reviewer catches it	fn-impact parseConfig shows every caller before the edit — agent fixes it proactively
AI agents	Leave dead exports and duplicate helpers behind after refactors	Dead code, cycles, and duplicates surface in real time via hooks and MCP queries
AI agents	Produce code that works but doesn't fit the codebase structure	context <name> -T returns source, deps, callers, and tests — the agent writes code that fits
CI pipelines	Catch test failures but miss structural degradation	check --staged fails the build when blast radius or complexity thresholds are exceeded
Developers	Inherit a codebase and grep for hours to understand what calls what	context handleAuth -T gives the same structured view agents use
Architects	Draw boundary rules that erode within weeks	manifesto and boundaries enforce architecture rules on every commit

Feature comparison

_{Comparison last verified: March 2026. Claims verified against each repo's README/docs. Full analysis: COMPETITIVE_ANALYSIS.md}

Capability	codegraph	joern	narsil-mcp	cpg	axon	GitNexus
Languages	34	~12	32	~10	3	13
MCP server	Yes	—	Yes	Yes	Yes	Yes
Dataflow + CFG + AST querying	Yes	Yes	Yes¹	Yes	—	—
Hybrid search (BM25 + semantic)	Yes	—	—	—	Yes	Yes
Git-aware (diff impact, co-change, branch diff)	All 3	—	—	—	All 3	—
Dead code / role classification	Yes	—	Yes	—	Yes	—
Incremental rebuilds	O(changed)	—	O(n)	—	Yes	Commit-level⁴
Architecture rules + CI gate	Yes	—	—	—	—	—
Security scanning (SAST / vuln detection)	Intentionally out of scope²	Yes	Yes	Yes	—	—
Zero config, npm install	Yes	—	Yes	—	Yes	Yes
Graph export (GraphML / Neo4j / DOT)	Yes	Yes	—	—	—	—
Open source + commercial use	Yes (Apache-2.0)	Yes (Apache-2.0)	Yes (MIT/Apache-2.0)	Yes (Apache-2.0)	Source-available³	Non-commercial⁵

^{¹ narsil-mcp added CFG and dataflow in recent versions. ² Codegraph focuses on structural understanding, not vulnerability detection — use dedicated SAST tools (Semgrep, CodeQL, Snyk) for that. ³ axon claims MIT in pyproject.toml but has no LICENSE file in the repo. ⁴ GitNexus skips re-index if the git commit hasn't changed, but re-processes the entire repo when it does — no per-file incremental parsing. ⁵ GitNexus uses the PolyForm Noncommercial 1.0.0 license.}

What makes codegraph different

	Differentiator	In practice
🤖	AI-first architecture	30-tool MCP server — agents query the graph directly instead of scraping the filesystem. One call replaces 20+ grep/find/cat invocations
🏷️	Role classification	Every symbol auto-tagged as entry/core/utility/adapter/dead/leaf — agents understand a symbol's architectural role without reading surrounding code
🔬	Function-level, not just files	Traces handleAuth() → validateToken() → decryptJWT() and shows 14 callers across 9 files break if decryptJWT changes
⚡	Always-fresh graph	Three-tier change detection: journal (O(changed)) → mtime+size (O(n) stats) → hash (O(changed) reads). Sub-second rebuilds — agents work with current data
💥	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
🌐	Multi-language, one graph	34 languages in a single graph — JS/TS, Python, Go, Rust, Java, C#, PHP, Ruby, C/C++, Kotlin, Swift, Scala, Bash, HCL, Elixir, Lua, Dart, Zig, Haskell, OCaml, F#, Gleam, Clojure, Julia, R, Erlang, Solidity, Objective-C, CUDA, Groovy, Verilog — agents don't need per-language tools
🧠	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 34 languages
🔓	Fully local, zero cost	No API keys, no accounts, no network calls. Optionally bring your own LLM provider — your code only goes where you choose

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🚀 Quick Start

npm install -g @optave/codegraph
cd your-project
codegraph build        # → .codegraph/graph.db created

That's it. The graph is ready. Now connect your AI agent.

For AI agents (primary use case)

Connect directly via MCP — your agent gets 30 tools to query the graph:

codegraph mcp          # 33-tool MCP server — AI queries the graph directly

Or 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

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

For developers

The same graph is available via CLI:

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/ops-codegraph-tool.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.

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✨ Features

	Feature	Description
🤖	MCP server	33-tool MCP server for AI assistants; single-repo by default, opt-in multi-repo
🎯	Deep context	context gives agents source, deps, callers, signature, and tests for a function in one call; audit --quick gives structural summaries
🏷️	Node role classification	Every symbol auto-tagged as entry/core/utility/adapter/dead/leaf based on connectivity — agents instantly know architectural role
📦	Batch querying	Accept a list of targets and return all results in one JSON payload — enables multi-agent parallel dispatch
💥	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
📍	Fast lookup	where shows exactly where a symbol is defined and used — minimal, fast
🔍	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
📊	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
🔄	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
⚡	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 34 languages
🧮	Complexity metrics	Cognitive, cyclomatic, nesting depth, Halstead, and Maintainability Index per function
🏘️	Community detection	Leiden 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
🔬	Dataflow analysis	Track how data moves through functions with flows_to, returns, and mutates edges — all 34 languages, included by default, skip with --no-dataflow
🧩	Control flow graph	Intraprocedural CFG construction for all 34 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 (designed for AI agents)

codegraph context <name>       # Full context: source, deps, callers, signature, tests
codegraph context <name> --depth 2 --no-tests  # Include callee source 2 levels deep
codegraph brief <file>            # Token-efficient file summary: symbols, roles, risk tiers
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             # Leiden 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 34 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
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)
--table	Output as auto-column aligned table
--csv	Output as CSV (RFC 4180, nested objects flattened)
--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	Imports	Exports	Call Sites	Heritage¹	Type Inference²	Dataflow
	.js, .jsx, .mjs, .cjs	✓	✓	✓	✓	✓	✓
	.ts, .tsx	✓	✓	✓	✓	✓	✓
	.py, .pyi	✓	✓	✓	✓	✓	✓
	.go	✓	✓	✓	✓	✓	✓
	.rs	✓	✓	✓	✓	✓	✓
	.java	✓	✓	✓	✓	✓	✓
	.cs	✓	✓	✓	✓	✓	✓
	.php, .phtml	✓	✓	✓	✓	✓	✓
	.rb, .rake, .gemspec	✓	✓	✓	✓	—³	✓
	.c, .h	✓	✓	✓	—⁴	—⁴	✓
	.cpp, .hpp, .cc, .cxx	✓	✓	✓	✓	—	✓
	.kt, .kts	✓	✓	✓	✓	—	✓
	.swift	✓	✓	✓	✓	—	✓
	.scala, .sc	✓	✓	✓	✓	—	✓
	.sh, .bash	✓	✓	✓	—⁴	—⁴	✓
	.ex, .exs	✓	✓	✓	—	—	✓
	.lua	✓	✓	✓	—	—	✓
	.dart	✓	✓	✓	✓	—	✓
	.zig	✓	✓	✓	—	—	✓
	.hs	✓	✓	✓	—	—	✓
	.ml, .mli	✓	✓	✓	—	—	✓
	.fs, .fsx, .fsi	✓	✓	✓	—	—	✓
	.gleam	✓	✓	✓	—	—	✓
	.clj, .cljs, .cljc	✓	✓	✓	—	—	✓
	.jl	✓	✓	✓	—	—	✓
	.r, .R	✓	✓	✓	—	—	✓
	.erl, .hrl	✓	✓	✓	—	—	✓
	.sol	✓	✓	✓	✓	—	✓
	.m	✓	✓	✓	✓	—	✓
	.cu, .cuh	✓	✓	✓	✓	—	✓
	.groovy, .gvy	✓	✓	✓	✓	—	✓
	.v, .sv	✓	✓	✓	—	—	✓
	.tf, .hcl	✓	—³	—³	—³	—³	—³

¹ Heritage = extends, implements, include/extend (Ruby), trait impl (Rust), receiver methods (Go). ² Type Inference extracts a per-file type map from annotations (const x: Router, MyType x, x: MyType) and new expressions, enabling the edge resolver to connect x.method() → Type.method(). ³ Not applicable — Ruby is dynamically typed; Terraform/HCL is declarative (no functions, classes, or type system). ⁴ Not applicable — C and Bash have no class/inheritance system. All languages have full parity between the native Rust engine and the WASM fallback.

⚙️ How It Works

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

1. Parse — tree-sitter parses every source file into an AST (native Rust engine or WASM fallback)
2. Extract — Functions, classes, methods, interfaces, imports, exports, call sites, parameters, properties, and constants are extracted
3. Resolve — Imports are resolved to actual files (handles ESM conventions, tsconfig.json path aliases, baseUrl)
4. Store — Everything goes into SQLite as nodes + edges with tree-sitter node boundaries, plus structural edges (contains, parameter_of, receiver)
5. Analyze (opt-in) — Complexity metrics, control flow graphs (--cfg), dataflow edges (--dataflow), and AST node storage
6. 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:

1. 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
2. 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
3. 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.

What incremental rebuilds refresh — and what they don't

Incremental builds re-parse changed files and rebuild their edges, structure metrics, and role classifications. But some data is only fully refreshed on a full rebuild:

Data	Incremental	Full rebuild
Symbols & edges for changed files	Yes	Yes
Reverse-dependency cascade (importers of changed files)	Yes	Yes
AST nodes, complexity, CFG, dataflow for changed files	Yes	Yes
Directory-level cohesion metrics	Partial (skipped for ≤5 files)	Yes
Advisory checks (orphaned embeddings, stale embeddings, unused exports)	Skipped	Yes
Build metadata persistence	Skipped for ≤3 files	Yes
Incremental drift detection	Skipped	Yes

When to run a full rebuild:

codegraph build --no-incremental   # Force full rebuild

• After large refactors (renames, moves, deleted files) — the reverse-dependency cascade handles most cases, but a full rebuild ensures nothing is stale
• If you suspect stale analysis data — complexity or dataflow results for files you didn't directly edit won't update incrementally
• Periodically — if you rely heavily on complexity, dataflow, roles --role dead, or communities queries, run a full rebuild weekly or after major merges
• After upgrading codegraph — engine, schema, or version changes trigger an automatic full rebuild, but if you skip versions you may want to force one

Codegraph auto-detects and forces a full rebuild when the engine, schema version, or codegraph version changes between builds. For everything else, incremental is the safe default — a full rebuild is a correctness guarantee, not a frequent necessity.

Detailed guide: See docs/guides/incremental-builds.md for a complete breakdown of what each build mode refreshes and recommended rebuild schedules.

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).

On the native path, Rust handles the entire hot pipeline end-to-end:

Phase	What Rust does
Parse	Parallel multi-file tree-sitter parsing via rayon (3.5× faster than WASM)
Extract	Symbols, imports, calls, classes, type maps, AST nodes — all in one pass
Analyze	Complexity (cognitive, cyclomatic, Halstead), CFG, and dataflow pre-computed per function during parse
Resolve	Import resolution with 6-level priority system and confidence scoring
Edges	Call, receiver, extends, and implements edge inference
DB writes	All inserts (nodes, edges, AST nodes, complexity, CFG, dataflow) via rusqlite — better-sqlite3 is lazy-loaded only for the WASM fallback path

The Rust crate (crates/codegraph-core/) exposes a NativeDatabase napi-rs class that holds a persistent rusqlite::Connection for the full build lifecycle, eliminating JS↔SQLite round-trips on every operation.

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 | query benchmarks | incremental benchmarks | resolution precision/recall):

Last updated: v3.9.6 (2026-04-30)

Metric	Native	WASM
Build speed	5.8 ms/file	28.3 ms/file
Query time	47ms	43ms
No-op rebuild	13ms	134ms
1-file rebuild	78ms	68ms
Query: fn-deps	3.4ms	2.4ms
Query: path	3.1ms	2.2ms
~50,000 files (est.)	~290.0s build	~1415.0s build
Resolution precision	90.5%	—
Resolution recall	42.0%	—

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

Per-language resolution precision/recall

Language	Precision	Recall	TP	FP	FN	Edges	Dynamic
javascript	100.0%	66.7%	12	0	6	18	14/28
typescript	100.0%	75.0%	15	0	5	20	—
bash	100.0%	100.0%	12	0	0	12	0/1
c	100.0%	100.0%	9	0	0	9	—
clojure	80.0%	26.7%	4	1	11	15	—
cpp	100.0%	57.1%	8	0	6	14	—
csharp	100.0%	52.6%	10	0	9	19	—
cuda	50.0%	33.3%	4	4	8	12	—
dart	0.0%	0.0%	0	0	18	18	—
elixir	0.0%	0.0%	0	0	15	15	—
erlang	100.0%	100.0%	12	0	0	12	—
fsharp	0.0%	0.0%	0	9	12	12	—
gleam	100.0%	26.7%	4	0	11	15	—
go	100.0%	69.2%	9	0	4	13	13/14
groovy	100.0%	7.7%	1	0	12	13	—
haskell	0.0%	0.0%	0	0	12	12	—
hcl	0.0%	0.0%	0	0	2	2	—
java	100.0%	52.9%	9	0	8	17	—
julia	0.0%	0.0%	0	0	15	15	—
kotlin	92.3%	63.2%	12	1	7	19	—
lua	100.0%	15.4%	2	0	11	13	—
objc	0.0%	0.0%	0	1	12	12	—
ocaml	100.0%	8.3%	1	0	11	12	—
php	100.0%	31.6%	6	0	13	19	—
python	100.0%	60.0%	9	0	6	15	15/15
r	100.0%	100.0%	11	0	0	11	—
ruby	100.0%	100.0%	11	0	0	11	11/11
rust	100.0%	35.7%	5	0	9	14	—
scala	100.0%	71.4%	5	0	2	7	—
solidity	33.3%	7.7%	1	2	12	13	—
swift	75.0%	42.9%	6	2	8	14	9/9
tsx	100.0%	100.0%	13	0	0	13	—
verilog	0.0%	0.0%	0	0	4	4	—
zig	0.0%	0.0%	0	0	15	15	—

By resolution mode (all languages):

Mode	Resolved	Expected	Recall
module-function	13	106	12.3%
receiver-typed	17	104	16.3%
static	66	93	71.0%
same-file	47	86	54.7%
interface-dispatched	7	12	58.3%
class-inheritance	0	4	0.0%
trait-dispatch	0	2	0.0%
package-function	1	1	100.0%

Lightweight Footprint

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

Dependency	What it does
better-sqlite3	SQLite driver (WASM engine; lazy-loaded, not used for native-engine reads)
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 (Core)

MCP Server

Codegraph is built around a Model Context Protocol server with 30 tools (31 in multi-repo mode) — the primary way agents consume the graph:

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 with all commands in the AI Agent Guide.

## Codegraph

This project uses codegraph for dependency analysis. The graph is at `.codegraph/graph.db`.

### Before modifying code:
1. `codegraph where <name>` — find where the symbol lives
2. `codegraph audit --quick <target>` — 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 graph (incremental by default)
- `codegraph map` — module overview · `codegraph stats` — graph health
- `codegraph query <name> -T` — call chain · `codegraph path <from> <to> -T` — shortest path
- `codegraph deps <file>` — file deps · `codegraph exports <file> -T` — export consumers
- `codegraph audit <target> -T` — full risk report · `codegraph triage -T` — priority queue
- `codegraph check --staged` — CI gate · `codegraph batch t1 t2 -T --json` — batch query
- `codegraph search "<query>"` — semantic search · `codegraph cycles` — cycle detection
- `codegraph roles --role dead -T` — dead code · `codegraph complexity -T` — metrics
- `codegraph dataflow <name> -T` — data flow · `codegraph cfg <name> -T` — control flow

### Flags
- `-T` — exclude test files (use by default) · `-j` — JSON output
- `-f, --file <path>` — scope to file · `-k, --kind <kind>` — filter kind

📋 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. The snippets below cover the most-used keys — see docs/guides/configuration.md for the full reference (every group, every key, every default).

{
  "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.

MCP tool filtering

Codegraph's MCP server exposes 30+ tools by default. For models with a small context window, you can shrink the schema by disabling tools you don't use:

{
  "mcp": {
    "disabledTools": ["execution_flow", "sequence", "communities", "co_changes"]
  }
}

Names are matched case-insensitively and a leading codegraph<digits>_ prefix (e.g. codegraph2_module_map) is stripped before comparison. Disabled tools are removed from tools/list and any tools/call invocation returns Unknown tool: <name>. See docs/guides/configuration.md#mcp-tool-filtering for the full tool catalog, and the rest of that guide for every other config option.

📖 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 TypeScript type-checker integration — type inference resolves annotations, new expressions, and assignment chains, but does not invoke tsc for overload resolution or complex generics
• 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:

1. 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
2. Foundation Hardening — Complete (v1.5.0) — parser registry, complete MCP, test coverage, enhanced config, multi-repo MCP
3. Analysis Expansion — Complete (v2.7.0) — complexity metrics, community detection, flow tracing, co-change, manifesto, boundary rules, check, triage, audit, batch, hybrid search
4. Deep Analysis & Graph Enrichment — Complete (v3.0.0) — dataflow analysis, intraprocedural CFG, AST node storage, expanded node/edge types, interactive viewer, exports command
5. Architectural Refactoring — Complete (v3.1.5) — unified AST analysis, composable MCP, domain errors, builder pipeline, graph model, qualified names, presentation layer, CLI composability
6. Resolution Accuracy — Complete (v3.3.1) — type inference, receiver type tracking, dead role sub-categories, resolution benchmarks, package.json exports, monorepo workspace resolution
7. TypeScript Migration — Complete (v3.4.0) — all 271 source files migrated from JS to TS, zero .js remaining
8. Native Analysis Acceleration — Complete (v3.5.0) — all build phases in Rust/rusqlite, sub-100ms incremental rebuilds, better-sqlite3 lazy-loaded as fallback only
9. Expanded Language Support — Complete (v3.8.0) — 23 new languages in 4 batches (11 → 34), dual-engine WASM + Rust support for all
10. Analysis Depth — TypeScript-native resolution, inter-procedural type propagation, field-based points-to analysis
11. Runtime & Extensibility — event-driven pipeline, plugin system, query caching, pagination
12. Quality, Security & Technical Debt — supply-chain security (SBOM, SLSA), CI coverage gates, timer cleanup, tech debt kill list
13. Intelligent Embeddings — LLM-generated descriptions, enhanced embeddings, module summaries
14. Natural Language Queries — codegraph ask command, conversational sessions
15. GitHub Integration & CI — reusable GitHub Action, LLM-enhanced PR review, SARIF output
16. Advanced Features — dead code detection, monorepo support, agentic search

🤝 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/ops-codegraph-tool.git
cd codegraph
npm install
npm test

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

📄 License

Apache-2.0

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