CodeGraph

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Supercharge Claude Code, Cursor, Codex, OpenCode, Hermes Agent, Gemini, Antigravity, Kiro, and GitHub Copilot with Semantic Code Intelligence

The fastest complete code graph · surgical context · built for how agents actually work · 100% local

  **Kernel powered by Rust**

Documentation & Website →

The CodeGraph platform is coming — for every PR, know exactly what to test, what could break, which flows are affected, and whether business logic is compromised.

_{Get early beta access to the hosted product · getcodegraph.com}

• Get Started
• Language Support
• Why CodeGraph?
• Key Features
• Framework-aware Routes
• Mixed iOS / React Native / Expo bridging
• Quick Start
• How It Works
• CLI Reference
• MCP Tools
• Library Usage
• Configuration
• Telemetry
• Verified releases
• Supported Platforms
• Supported Agents
• Supported Languages
• Measured cross-file coverage
• Troubleshooting
• License

No Node.js required — one command grabs the right build for your OS:

# macOS / Linux
curl -fsSL https://raw.githubusercontent.com/colbymchenry/codegraph/main/install.sh | sh

# Windows (PowerShell)
irm https://raw.githubusercontent.com/colbymchenry/codegraph/main/install.ps1 | iex

npm i -g @colbymchenry/codegraph

In a new terminal, run the installer to connect CodeGraph to the agents you use:

codegraph install

_{Detects and auto-configures Claude Code, Cursor, Codex CLI, opencode, Hermes Agent, Gemini CLI, Antigravity IDE, Kiro, and GitHub Copilot (VS Code, Copilot CLI, JetBrains IDEs) — wiring the CodeGraph MCP server into each. This is the step that connects CodeGraph to your agent; installing the CLI in step 1 does not do it on its own. It only wires up your agent — it does not index any code; building each project's graph is the separate codegraph init in step 3. (Shortcut: npx @colbymchenry/codegraph downloads and runs this in one go.)}

cd your-project
codegraph init

_{codegraph init creates the local .codegraph/ directory and builds the full graph in the same step — one command, done.}

Auto-sync is enabled by default. CodeGraph watches the project and updates the graph on every file change — while your agent edits code, or you add, modify, or delete files. The index is never stale, and there is nothing to re-run.

Changed your mind? One command removes CodeGraph from every agent it configured and the CLI itself — every install it finds (standalone bundle, npm global package, launcher link), shown to you before anything is deleted:

codegraph uninstall

Pass --keep-cli to remove only the agent configurations and keep the CLI installed.

_{Reverses the installer — strips CodeGraph's MCP server config, instructions, and permissions from each configured agent. Your project indexes (.codegraph/) are left untouched; remove those per-project with codegraph uninit. Use --target to remove from specific agents, or --yes to run non-interactively.}

Every language below gets the same treatment — full structural extraction and cross-file resolution into one graph, no per-language setup:

_{Per-language details — extensions, frameworks, and what exactly gets extracted — in Supported Languages.}

When an AI agent needs to understand code — to answer a question or make a change — it discovers structure the slow way: grep, glob, and Read, one file at a time, rebuilding call paths and dependencies by hand. That's a pile of tool calls and round-trips before it even starts the real work.

CodeGraph hands the agent the exact code it needs in one call. It's a pre-built knowledge graph of every symbol, call edge, and dependency in your codebase — so instead of crawling files, the agent asks one question and gets back the relevant source, the call paths between those symbols (including dynamic-dispatch hops grep can't follow), and the blast radius of a change. Surgical context, not a file-by-file search — which means fewer tool calls and faster answers on every codebase, large or small.

A note on cost: CodeGraph's win on every codebase is precision — the agent stops crawling files and answers from the graph. On current models that precision is also a large direct saving: the 2026-08 re-measurement, on a harness that blocks the CLI in both arms, put it at 44% lower cost and 62% fewer tokens on average across the seven benchmark repos, because a strong model without the graph burns its budget re-deriving structure. Cost tracks how much discovery a question demands more than raw repo size: 57–78% on questions the file-reading agent needed 28–43 tool calls to answer, near-even where it got there in 7.

A note on context: the numbers above measure throughput — tokens processed, tools called, dollars spent to reach one answer. They don't measure what is still sitting in your context window afterward, and on that axis CodeGraph costs more, not less. Across the same seven repos in multi-turn sessions, CodeGraph's responses leave about 80% more retrieval context resident at the end of a session than a file-reading agent's do — on VS Code, 67k tokens against 18k. The mechanism is the same one that makes it fast: CodeGraph returns one dense, verbatim payload that answers the question and then stays in the window, where a grep-and-read agent churns through many small results that get evicted. Fewer tokens processed and a larger persistent footprint are both real at once. If you run long sessions in a small window, budget for it. Measured per-repo: docs/benchmarks/residual-context-occupancy.md.

Tested across 7 real-world open-source codebases spanning 7 languages, comparing an agent (Claude Code, headless) answering one architecture question with and without CodeGraph, at the median of 4 runs per arm. Re-measured 2026-08-05 on Claude Opus 4.8 against the current build, on a harness that blocks the codegraph CLI in both arms — contamination row: 0 of 28 without-arm runs.

The universal win — every repo, every size: 88% fewer tool calls · 53% faster · 62% fewer tokens · 44% cheaper · file reads cut to zero on all seven repos.

With the index available, the agent answers from one to four codegraph_explore calls and stops. Without it, the agent burns its budget on discovery — up to 43 tool calls and 19 file reads re-deriving what the graph already knew. Every repo was faster with CodeGraph in this measurement — by 35% on the narrowest question, by 3.6× on the widest.

_{¹ Cost tracks how much discovery the question demanded, which is why it varies far more than the other columns: 57–78% on repos where the file-reading arm needed 28–43 tool calls, but only 13% on Django and even on Gin, where it got there in 14 and 7. The with-arm still answered in 3 and 1 calls with zero file reads. File reads = median files opened — the surgical-context win in one column: the agent never reads a file on any of the seven repos when CodeGraph is present.}

CodeGraph's parsing engine is a native Rust kernel: 20 languages — TypeScript, JavaScript, Java, Python, Go, C, C++, Rust, C#, Ruby, PHP, Swift, Kotlin, Scala, Dart, R, Lua, Luau (Metal and CUDA ride the C++ path) — parse in compiled code with one boundary crossing per file. Every language shipped only after its graphs proved byte-for-byte identical to the reference engine on real repositories, from small libraries up to the Linux kernel; platforms without a prebuilt binary and files with syntax errors fall back per-file automatically, same graph either way.

And it scales itself to the machine it's on. Worker pools, parallel resolution, and analysis caches are sized from what the system actually has — real core counts (container/cgroup-aware, so a VPS that grants 2 cores gets sized for 2, not the host's 64), honestly-measured available RAM on macOS and Linux, and the measured cost of your project's resolution work:

• On a workstation: the full parallel pipeline — native parse workers, a multi-worker resolver pool that engages the moment it pays for itself, memory-gated analysis caches. The Swift compiler repository (27k files of Swift and C++) fresh-indexes in about 100 seconds; a one-file edit re-syncs in ~4.
• On a 2-core / 6GB VPS: the same graph, from a pipeline tuned to finish — the Linux kernel (70k files, 2M symbols, 6.4M relationships) indexes to completion in under 12 minutes where RAM-first designs run out of memory before reaching 1%.
• Every day after day one: saving a file updates the graph in well under a second — the watcher fires 300ms after a lone save and syncs exactly what changed (~0.3s of work on a 4,400-file project, ~0.4s on the 27,000-file Swift compiler repo), never re-scanning the tree. Measured against the fastest competing indexer's re-index-on-change: 2–7× faster on medium and larger repos across a 31-repo, 30-language benchmark — and the gap widens with repo size, because their cost grows with the repository and ours grows with the change.

agent writes src/Widget.ts
  → watcher fires (<100ms)
  → debounce (default 2s)
  → sync; Widget.ts is in the index
  → next agent query sees it

CodeGraph detects web-framework routing files and emits route nodes linked by references edges to their handler classes or functions. Querying callers of a view/controller now surfaces the URL pattern that binds it.

These frameworks additionally emit navigates edges: the function that sends a user somewhere is linked to the screen it names, so "where does tapping this go" is one hop in the graph rather than a search. Each reads a literal destination — a computed one, or a path no route serves, is left unresolved rather than guessed — and a link written in markup is marked as inferred.

In a repository holding several apps, each app's routes are matched only against navigation written inside that app.

Real iOS and React Native codebases live across multiple languages — a Swift caller invokes an Objective-C selector that's been auto-bridged, a JS file calls into a native module via the React Native bridge, a JSX component delegates to a native view manager. Static tree-sitter extraction stops at each language boundary. CodeGraph bridges them so codegraph_explore connects the flow end-to-end across the gap — call paths and blast radius cross the boundary instead of stopping at it.

Validated on real codebases (small + medium + large for each bridge):

Every bridge hop says how it got into the graph. A hop matched by a bridge resolver carries metadata.resolvedBy: 'framework' and metadata.framework naming the resolver (swift-objc-bridge, react-native-bridge, expo-modules-js, fabric-view). A synthesized channel is tagged provenance:'heuristic' with metadata.synthesizedBy (rn-event-channel, fabric-native-impl).

npx @colbymchenry/codegraph

The installer will:

• Ask which agent(s) to configure — auto-detects installed ones from: Claude Code, Cursor, Codex CLI, opencode, Hermes Agent, Gemini CLI, Antigravity IDE, Kiro, GitHub Copilot (VS Code, Copilot CLI, JetBrains IDEs)
• Prompt to install codegraph on your PATH (so agents can launch the MCP server)
• Ask whether configs apply to all your projects or just this one
• Write each chosen agent's MCP server config, plus a small marker-fenced CodeGraph section in the agent's instructions file (CLAUDE.md / AGENTS.md / GEMINI.md) — that's how subagents and non-MCP agents learn the codegraph explore command, since the MCP server's own guidance only reaches the main agent. Removed cleanly by codegraph uninstall.
• Set up auto-allow permissions when Claude Code is one of the targets

The installer wires up your agents only — it does not index your code. After it finishes, build each project's graph yourself with codegraph init (step 3). One global codegraph install covers every project; you run codegraph init once per project.

Non-interactive (scripting / CI):

codegraph install --yes                              # auto-detect agents, install global
codegraph install --yes --init                       # same, then build the current project's index (one-shot bootstrap)
codegraph install --target=cursor,claude --yes       # explicit target list
codegraph install --target=auto --location=local     # detected agents, project-local
codegraph install --target=copilot-vscode,copilot-cli,copilot-jetbrains --yes  # GitHub Copilot everywhere
codegraph install --print-config codex               # print snippet, no file writes
codegraph install --print-config copilot-vscode      # same, for Copilot in VS Code

Restart your agent (Claude Code / Cursor / Codex CLI / opencode / Hermes Agent / Gemini CLI / Antigravity IDE / Kiro / VS Code, the Copilot CLI, or your JetBrains IDE for GitHub Copilot) for the MCP server to load.

cd your-project
codegraph init

Builds the per-project knowledge graph index, which then auto-syncs on every file change. A single global codegraph install works in every project you open — no need to re-run the installer per project. Add --yes to skip every prompt (scripts / CI / container bootstraps).

That's it — your agent will use CodeGraph tools automatically when a .codegraph/ directory exists.

npm install -g @colbymchenry/codegraph

{
  "mcpServers": {
    "codegraph": {
      "type": "stdio",
      "command": "codegraph",
      "args": ["serve", "--mcp"],
      "alwaysLoad": true
    }
  }
}

{
  "permissions": {
    "allow": [
      "mcp__codegraph__*"
    ]
  }
}

┌───────────────────────────────────────────────────────────────────┐
│                            Claude Code                            │
│                                                                   │
│   "How does a request reach the database?"                        │
│       calls CodeGraph tools directly — no Explore sub-agent       │
│                                 │                                 │
└─────────────────────────────────┬─────────────────────────────────┘
                                  │
                                  ▼
┌───────────────────────────────────────────────────────────────────┐
│                        CodeGraph MCP Server                       │
│                                                                   │
│ explore  ·  one call → verbatim source + call flow + blast radius │
│                                 │                                 │
│                                 ▼                                 │
│                       SQLite knowledge graph                      │
│          symbols · edges · files · FTS5 full-text search          │
└───────────────────────────────────────────────────────────────────┘

1. Extraction — a native Rust kernel parses source with tree-sitter grammars compiled into it, extracting nodes (functions, classes, methods) and edges (calls, imports, extends, implements) for 20 languages; remaining languages and per-file fallbacks use the same extraction logic on the portable engine, producing identical graphs.

2. Storage — Everything goes into a local SQLite database (.codegraph/codegraph.db) with FTS5 full-text search.

3. Resolution — After extraction, references are resolved: function calls → definitions, imports → source files, class inheritance, and framework-specific patterns.

4. Auto-Sync — The MCP server watches your project using native OS file events. Changes are debounced (2-second quiet window), filtered to source files only, and incrementally synced. The graph stays fresh as you code — no configuration needed.

codegraph                         # Run interactive installer
codegraph install                 # Run installer (explicit)
codegraph uninstall               # Remove CodeGraph from your agents AND the CLI (--keep-cli for configs only)
codegraph init [path]             # Initialize a project + build its graph (one step)
codegraph uninit [path]           # Remove CodeGraph from a project (--force to skip prompt)
codegraph index [path]            # Full index (--force to re-index, --quiet for less output)
codegraph sync [path]             # Incremental update
codegraph status [path]           # Show statistics
codegraph unlock [path]           # Remove a stale lock file that's blocking indexing
codegraph query <search>          # Search symbols (--kind, --limit, --json)
codegraph explore <query>         # Relevant symbols' source + call paths in one shot (same output as the codegraph_explore MCP tool)
codegraph node <symbol|file>      # One symbol's source + callers, or read a file with line numbers (same output as codegraph_node)
codegraph files [path]            # Show file structure (--format, --filter, --max-depth, --json)
codegraph callers <symbol>        # Find what calls a function/method (--limit, --json)
codegraph callees <symbol>        # Find what a function/method calls (--limit, --json)
codegraph impact <symbol>         # Analyze what code is affected by changing a symbol (--depth, --json)
codegraph affected [files...]     # Find test files affected by changes (see below)
codegraph daemon                  # Manage background daemons — pick one to stop (alias: daemons)
codegraph telemetry [on|off]      # Show or change anonymous usage telemetry
codegraph upgrade [version]       # Update to the latest release (--check, --force)
codegraph version                 # Print the installed version (also -v, --version)
codegraph help [command]          # Show help, optionally for one command

Traces import dependencies transitively to find which test files are affected by changed source files.

codegraph affected src/utils.ts src/api.ts         # Pass files as arguments
git diff --name-only | codegraph affected --stdin   # Pipe from git diff
codegraph affected src/auth.ts --filter "e2e/*"     # Custom test file pattern

CI/hook example:

#!/usr/bin/env bash
AFFECTED=$(git diff --name-only HEAD | codegraph affected --stdin --quiet)
if [ -n "$AFFECTED" ]; then
  npx vitest run $AFFECTED
fi

When running as an MCP server, CodeGraph exposes a single tool — codegraph_explore. Measured agent behavior showed that one strong tool steers agents better than a menu of narrower ones — fewer mis-picks, and it saves context every session:

The other tools (codegraph_node, codegraph_search, codegraph_callers, codegraph_callees, codegraph_impact, codegraph_files, codegraph_status) stay fully functional but unlisted by default — everything they return already arrives inline on codegraph_explore (its blast-radius section, the relationship map, a symbol's body as its callee list). Re-enable any of them for the MCP surface with the CODEGRAPH_MCP_TOOLS environment variable (e.g. CODEGRAPH_MCP_TOOLS=explore,node,search,callers), or use their CLI equivalents (codegraph node / query / callers / callees / impact / files / status).

Even when the server's own root has no .codegraph/ index, the tools stay available: pass projectPath to query any indexed project — a sub-service in a monorepo, or a second repo — in the same session. A path that has no index returns clean guidance to use built-in tools instead, so nothing fails loudly, and indexing stays your decision.

CodeGraph can be embedded directly. The npm package re-exports its programmatic API, so both import and require resolve the CodeGraph class in your own process — handy for embedding it in an app (e.g. an Electron main process).

import CodeGraph from '@colbymchenry/codegraph';
// CommonJS works too:
//   const { CodeGraph } = require('@colbymchenry/codegraph');

const cg = await CodeGraph.init('/path/to/project');
// Or: const cg = await CodeGraph.open('/path/to/project');

await cg.indexAll({
  onProgress: (p) => console.log(`${p.phase}: ${p.current}/${p.total}`)
});

const results = cg.searchNodes('UserService');
const callers = cg.getCallers(results[0].node.id);
const context = await cg.buildContext('fix login bug', { maxNodes: 20, includeCode: true, format: 'markdown' });
const impact = cg.getImpactRadius(results[0].node.id, 2);

cg.watch();   // auto-sync on file changes
cg.unwatch(); // stop watching
cg.close();

Lower-level building blocks are exported from the same entry point for callers that drive the graph directly: DatabaseConnection, QueryBuilder, getDatabasePath, initGrammars / loadGrammarsForLanguages, and FileLock.

Embedding requirements

• Install from npm (npm i @colbymchenry/codegraph) so the matching per-platform package — which carries the compiled library and its dependencies — is fetched alongside the shim.
• The API runs on your runtime, so it needs Node 22.5+ for the built-in node:sqlite (Electron qualifies when its bundled Node is 22.5+). The CLI and MCP server are unaffected — they run on the self-contained bundled runtime.
• TypeScript types ship with the package. As with any Node-targeting library, keep @types/node available and skipLibCheck: true (the common default).

Next to none — CodeGraph is zero-config by default, with nothing to write or keep in sync to get started. Language support is automatic from the file extension; there's nothing to wire up per language. The one optional file is for mapping custom file extensions.

What it skips out of the box:

• Dependency, build, and cache directories — node_modules, vendor, dist, build, target, .venv, Pods, .next, and the like across every supported stack — so the graph is your code, not third-party noise. This holds even with no .gitignore.
• Anything in your .gitignore — honored in git repos via git, and in non-git projects by reading .gitignore directly (root and nested).
• Files larger than 1 MB — generated bundles, minified JS, vendored blobs.

To keep something else out, add it to .gitignore. To pull a default-excluded directory back in (say you really do want a vendored dependency indexed), add a negation — !vendor/. The defaults apply uniformly, so committing a dependency or build directory doesn't force it into the graph; the .gitignore negation is the explicit opt-in.

.gitignore can't drop a directory you've committed, though. For a vendored theme or SDK that's checked into the repo (e.g. a Metronic theme under static/), list it under exclude in codegraph.json — gitignore-style patterns, matched against repo-root-relative paths, honored on index, sync, and watch:

{
  "exclude": ["static/", "**/vendor/**"]
}

Conversely, when real source is gitignored on purpose — a project under a second VCS (SVN, Perforce) that .gitignores its own source so it stays out of Git — force it back in with include (the opposite of exclude; includeIgnored only revives embedded git repos, not plain source):

{
  "include": ["Tools/", "Local/typescript/"]
}

CodeGraph discovers those files off disk, overriding .gitignore, on index, sync, and watch. An explicit exclude still wins, and built-in skips (node_modules, dist, .git) are never re-included.

Sometimes a directory shouldn't leave the index — you still want to find things in it — it just shouldn't outrank your real code. A scripts/ or optional-skills/ tree whose helpers use generic names (usage, status, run) can win on an exact name match and crowd out the product code that actually answers the query. Name those trees under deprioritize:

{
  "deprioritize": ["optional-skills/", "scripts/"]
}

This is the ranking counterpart to exclude: those paths stay indexed and findable — searching for them directly still works — they just stop winning against first-party code. It applies to query / search and to explore's ranking. It is not a filter: unlike the built-in example/, sample/, fixture/, benchmark/ and demo/ handling — which also drops those files from some result sets outright — deprioritize only ever changes rank. Reach for exclude when you want something gone.

If your project uses a non-standard extension for a supported language — say .dota_lua for Lua, or .tpl for PHP — those files are skipped by default, because the extension isn't one CodeGraph recognizes. Map them with an optional codegraph.json at your project root:

{
  "extensions": {
    ".dota_lua": "lua",
    ".tpl": "php"
  }
}

Each value is a supported language id. The mappings merge on top of the built-in defaults and win on conflict, so you can also re-point a built-in (e.g. ".h": "cpp"). Commit the file to share the mapping with your team. A typo'd language or a malformed file is warned about and skipped — it never breaks indexing — and a project with no codegraph.json behaves exactly as before. Re-index (codegraph index) after adding or changing mappings.

CodeGraph collects anonymous usage statistics — which tools and commands get used, which languages get indexed — to guide where language and agent support work goes. Never any code, paths, file or symbol names, queries, or IP addresses; usage is aggregated locally into daily totals before anything is sent, and the ingest endpoint is public code in this repo that enforces the documented field list. The installer asks up front; turn it off any time:

codegraph telemetry off    # or: CODEGRAPH_TELEMETRY=0, or DO_NOT_TRACK=1

TELEMETRY.md lists every field, with the off-switches and the full data-handling story.

Every artifact is built and published by the public Release workflow — never from a laptop — and carries cryptographic proof of it:

• npm packages are published via trusted publishing (OIDC — no long-lived npm tokens exist that could be stolen) with provenance attestations linking every version to the exact commit and workflow run that built it. Verify what's installed:

  npm audit signatures

• GitHub Release bundles (and SHA256SUMS) carry signed build attestations (SLSA v1.0 Build Level 2). Verify any downloaded bundle:

  gh attestation verify codegraph-darwin-arm64.tar.gz -R colbymchenry/codegraph

Releases published before July 2026 predate this pipeline and don't carry attestations.

Every release ships a self-contained build (bundled Node runtime — nothing to compile) for all three desktop OSes, on both Intel/AMD (x64) and ARM (arm64):

See Get Started for the one-line install commands.

The interactive installer auto-detects and configures each of these — wiring up the MCP server (which delivers its own usage guidance, so no instructions file is written):

• Claude Code
• Cursor
• Codex CLI
• opencode — MCP entry is OpenCode 2's mcp.servers.codegraph with codemode: false (keeps codegraph_explore on the native tool list; codegraph install migrates the older mcp.codegraph shape)
• Hermes Agent
• Gemini CLI
• Antigravity IDE
• Kiro
• GitHub Copilot — Copilot Chat in VS Code (copilot-vscode), the Copilot CLI (copilot-cli), and the Copilot plugin in JetBrains IDEs (copilot-jetbrains)

Impact and blast-radius queries are only as good as the dependency graph behind them, so coverage is measured rather than asserted. Fair coverage = the share of symbol-bearing source files that have at least one resolved cross-file dependent — something that imports, calls, references, or (through a framework convention) routes to them — on a real-world benchmark repo per language. The residual is always a genuine static-analysis frontier (runtime dynamic dispatch, reflection / DI containers, framework-convention entry points, vendored third-party code), never hidden by gaming the denominator.

Framework routing is validated the same way, on a canonical app per framework: Express 100%, FastAPI 98%, Flask 100%, NestJS 96.8%, Gin 96.5%, Axum 100%, Rocket 93.8%, Vapor 100%, Laravel 92%, Rails 89.6%, React Router 100% — and the convention/reflection-heavy ones at their honest static-analysis ceiling: ASP.NET 83.9%, Spring 83.3%, Drupal 78.9%, Play 76.3%, Django 74.1%. SvelteKit, Vue/Nuxt, and Astro use file-based routing, so their page/endpoint coverage is the Svelte/SvelteKit (100%), Vue/Nuxt (93.5%), and Astro (93.0% — every src/pages/ file maps to a route node on the two validation repos) figures in the table above.

"CodeGraph not initialized" — Run codegraph init in your project directory first.

Indexing is slow — Check that node_modules and other large directories are excluded. Use --quiet to reduce output overhead.

MCP hits database is locked — current builds shouldn't: CodeGraph bundles its own Node runtime and uses Node's built-in node:sqlite in WAL mode, where concurrent reads never block on a writer. If you still see it:

• You're on an old (pre-0.9) install. Reinstall to get the bundled runtime — curl -fsSL https://raw.githubusercontent.com/colbymchenry/codegraph/main/install.sh | sh (macOS/Linux), irm https://raw.githubusercontent.com/colbymchenry/codegraph/main/install.ps1 | iex (Windows), or npm i -g @colbymchenry/codegraph@latest.
• codegraph status shows Journal: other than wal — WAL couldn't be enabled on this filesystem (common on network shares and WSL2 /mnt), so reads can block on writes. Move the project (with its .codegraph/ folder) onto a local disk.

MCP server not connecting — Your agent starts the server itself, so you don't launch it by hand. Make sure the project is initialized and indexed (codegraph status) and that the path in your MCP config is correct. If it still won't connect, re-run codegraph install to rewrite the config.

Two codegraph serve --mcp on one project fight over the index / auto-sync stops — CodeGraph allows one live MCP writer per project (the shared background daemon, or a single direct-mode process). Extra clients should proxy to that daemon. If you set CODEGRAPH_NO_DAEMON=1, run only one serve --mcp for that project; a second instance exits with a clear writer-lock error (see writer.pid under .codegraph/). Prefer leaving the daemon enabled so multiple MCP hosts share one watcher.

MCP tool calls fail with Transport closed while codegraph status/sync are healthy — almost always WSL2 with the project on a Windows drive (a /mnt/c or /mnt/d path), where the local socket CodeGraph uses to share one background server across sessions is unreliable. CodeGraph now falls back to serving the session in-process instead of dropping the connection, but if you still hit it, set CODEGRAPH_NO_DAEMON=1 in your MCP server's environment to skip the shared server entirely (each session runs in its own process). Moving the project onto the Linux-native filesystem (e.g. under ~/ instead of /mnt/) restores the shared server.

Missing symbols — The MCP server auto-syncs on save (wait a couple seconds). Run codegraph sync manually if needed. Check that the file's language is supported and isn't inside a .gitignored or default-excluded directory (e.g. node_modules, dist).

Sharing one checkout between Windows and WSL — Don't point both at the same .codegraph/: the background-server lock and the SQLite index are tied to the OS that wrote them, and SQLite locking across the WSL2/Windows filesystem boundary is unreliable (WSL reports it as a disk I/O error). For a project on a Windows drive (a /mnt/c/… path), WSL keeps its own index automatically: an index first built from WSL goes in .codegraph-wsl/, leaving .codegraph/ to Windows. An index already in .codegraph/ stays where it is, so if Windows built that one, give WSL its own by setting CODEGRAPH_DIR=.codegraph-wsl in WSL and running codegraph init there. CODEGRAPH_DIR always picks the name when set, on either side. CodeGraph skips any sibling .codegraph-* directory when indexing and watching, so the two never trip over each other.

Very large repositories (hundreds of thousands of files), or a large .codegraph/codegraph.db-wal file — The -wal file is SQLite's write-ahead log: writes waiting to be folded into codegraph.db. While a big index is being built, CodeGraph lets it grow in proportion to the index (soft threshold = the larger of 256 MB and a quarter of the index size, up to 2 GB) before folding it back, because folding too often is what made large indexes slow on ordinary disks. At rest it is trimmed to 64 MB, and a leftover from a killed session is folded and trimmed the next time the project opens — the index itself has no size limit. Two environment variables tune this: CODEGRAPH_WAL_VALVE_MB (the soft threshold during indexing) and CODEGRAPH_WAL_HEAL_MB (the resting size and the trim threshold). CODEGRAPH_WAL_VALVE_DEBUG=1 prints every decision to stderr.

MIT