# GitNexus

**⚠️ Important Notice:** GitNexus has NO official cryptocurrency, token, or coin. Any token/coin using the GitNexus name on Pump.fun or any other platform is **not affiliated with, endorsed by, or created by** this project or its maintainers. Do not purchase any cryptocurrency claiming association with GitNexus.

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  <p><strong>Enterprise (SaaS & Self-hosted)</strong> - <a href="https://akonlabs.com">akonlabs.com</a></p>

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**Building nervous system for agent context.**

Indexes any codebase into a knowledge graph — every dependency, call chain, cluster, and execution flow — then exposes it through smart tools so AI agents never miss code.

https://github.com/user-attachments/assets/172685ba-8e54-4ea7-9ad1-e31a3398da72

> _Like DeepWiki, but deeper._ DeepWiki helps you _understand_ code. GitNexus lets you _analyze_ it — because a knowledge graph tracks every relationship, not just descriptions.

**TL;DR:** The **Web UI** is a quick way to chat with any repo. The **CLI + MCP** is how you make your AI agent actually reliable — it gives Cursor, Claude Code, Antigravity, Codex, and friends a deep architectural view of your codebase so they stop missing dependencies, breaking call chains, and shipping blind edits. Even smaller models get full architectural clarity, making it compete with Goliath models.

---

## Star History

[![Star History Chart](https://api.star-history.com/svg?repos=abhigyanpatwari/GitNexus&type=date&legend=top-left)](https://www.star-history.com/#abhigyanpatwari/GitNexus&type=date&legend=top-left)

## Two Ways to Use GitNexus

|             | **CLI + MCP**                                                         | **Web UI**                                                           |
| ----------- | --------------------------------------------------------------------- | -------------------------------------------------------------------- |
| **What**    | Index repos locally, connect AI agents via MCP                        | Visual graph explorer + AI chat in browser                           |
| **For**     | Daily development with Cursor, Claude Code, Antigravity, Codex, Windsurf, OpenCode | Quick exploration, demos, one-off analysis                           |
| **Scale**   | Full repos, any size                                                  | Limited by browser memory (~5k files), or unlimited via backend mode |
| **Install** | `npm install -g gitnexus`                                             | No install — [gitnexus.vercel.app](https://gitnexus.vercel.app)      |
| **Storage** | LadybugDB native (fast, persistent)                                   | LadybugDB WASM (in-memory, per session)                              |
| **Parsing** | Tree-sitter native bindings                                           | Tree-sitter WASM                                                     |
| **Privacy** | Everything local, no network                                          | Everything in-browser, no server                                     |

> **Bridge mode:** `gitnexus serve` connects the two — the web UI auto-detects the local server and can browse all your CLI-indexed repos without re-uploading or re-indexing.

---

## Enterprise

GitNexus is available as an **enterprise offering** - either as a fully managed **SaaS** or a **self-hosted** deployment. Also available for **commercial use** of the OSS version with proper licensing.

Enterprise includes:

- **PR Review** - automated blast radius analysis on pull requests
- **Auto-updating Code Wiki** - always up-to-date documentation (Code Wiki is also available in OSS)
- **Auto-reindexing** - knowledge graph stays fresh automatically
- **Multi-repo support** - unified graph across repositories
- **OCaml support** - additional language coverage
- **Priority feature/language support** - request new languages or features

**Upcoming:**

- Auto regression forensics
- End-to-end test generation

👉 Learn more at [akonlabs.com](https://akonlabs.com)

💬 For commercial licensing or enterprise inquiries, ping us on [Discord](https://discord.gg/AAsRVT6fGb) or drop an email at founders@akonlabs.com

---

## Development

- [ARCHITECTURE.md](ARCHITECTURE.md) — packages, index → graph → MCP flow, where to change code
- [RUNBOOK.md](RUNBOOK.md) — analyze, embeddings, stale index, MCP recovery, CI snippets
- [GUARDRAILS.md](GUARDRAILS.md) — safety rules and operational “Signs” for contributors and agents
- [CONTRIBUTING.md](CONTRIBUTING.md) — license, setup, commits, and pull requests
- [TESTING.md](TESTING.md) — test commands for `gitnexus` and `gitnexus-web`

## CLI + MCP (recommended)

The CLI indexes your repository and runs an MCP server that gives AI agents deep codebase awareness.

### Quick Start

```bash
# Index your repo (run from repo root)
npx gitnexus analyze
```

That's it. This indexes the codebase, installs agent skills, registers Claude Code hooks, and creates `AGENTS.md` / `CLAUDE.md` context files — all in one command.

> **On npm 11.x?** `npx` can crash during install with `Cannot destructure property 'package' of 'node.target'` (an npm/arborist bug, before GitNexus runs). Use pnpm instead — it builds the native deps explicitly:
>
> ```bash
> pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze
> ```
>
> Or install globally (`npm install -g gitnexus@latest`) and run `gitnexus analyze`. See [#1939](https://github.com/abhigyanpatwari/GitNexus/issues/1939).

To configure MCP for your editor, run `npx gitnexus setup` once — or set it up manually below.

> **Faster install (no C++ toolchain needed):** set `GITNEXUS_SKIP_OPTIONAL_GRAMMARS=1` before `npm install -g gitnexus` to skip vendored grammar materialize/build (`tree-sitter-dart`, `tree-sitter-proto`, `tree-sitter-swift`). Dart/Proto/Swift files won't be parsed, but install completes in seconds without `python3`/`make`/`g++`. Strict `=1` only — any other value falls through to the rebuild.

### MCP Setup

`gitnexus setup` auto-detects your editors and writes the correct global MCP config. You only need to run it once.

### Editor Support

| Editor               | MCP | Skills | Hooks (auto-augment)                                                                    | Support      |
| -------------------- | --- | ------ | --------------------------------------------------------------------------------------- | ------------ |
| **Claude Code**      | Yes | Yes    | Yes (PreToolUse + PostToolUse)                                                          | **Full**     |
| **Cursor**           | Yes | Yes    | Yes (postToolUse, [manual install](gitnexus-cursor-integration/README.md#hook-install)) | **Full**     |
| **Antigravity** (Google) | Yes | Yes | Yes (AfterTool, [Gemini CLI hooks schema](https://geminicli.com/docs/hooks/reference/))[¹](#fn-antigravity-hooks) | **Full**     |
| **Codex**            | Yes | Yes    | —                                                                                       | MCP + Skills |
| **Windsurf**         | Yes | —      | —                                                                                       | MCP          |
| **OpenCode**         | Yes | Yes    | —                                                                                       | MCP + Skills |

> **Claude Code** gets the deepest integration: MCP tools + agent skills + PreToolUse hooks that enrich searches with graph context + PostToolUse hooks that detect a stale index after commits and prompt the agent to reindex.

<a id="fn-antigravity-hooks"></a>
> ¹ **Antigravity hooks** follow the [Gemini CLI hooks reference](https://geminicli.com/docs/hooks/reference/) (Antigravity 2.0 is the documented successor to Gemini CLI). Augmentation runs in `AfterTool` because `BeforeTool` has no context-injection channel in the Gemini contract — the agent sees graph context appended to the tool result via `hookSpecificOutput.additionalContext`. Stale-index hints land in the same channel after a successful `git commit/merge/rebase/cherry-pick/pull`. The schema may evolve if Antigravity-specific hook docs diverge from Gemini CLI's; the implementation will track those changes.

## Community Integrations

Built by the community — not officially maintained, but worth checking out.

| Project                                                                       | Author                                                 | Description                                                             |
| ----------------------------------------------------------------------------- | ------------------------------------------------------ | ----------------------------------------------------------------------- |
| [pi-gitnexus](https://github.com/tintinweb/pi-gitnexus)                       | [@tintinweb](https://github.com/tintinweb)             | GitNexus plugin for [pi](https://pi.dev) — `pi install npm:pi-gitnexus` |
| [gitnexus-stable-ops](https://github.com/ShunsukeHayashi/gitnexus-stable-ops) | [@ShunsukeHayashi](https://github.com/ShunsukeHayashi) | Stable ops & deployment workflows (Miyabi ecosystem)                    |

> Have a project built on GitNexus? Open a PR to add it here!

If you prefer manual configuration:

> **Recommended for fastest startup:** install gitnexus globally (`npm i -g gitnexus`) and run `gitnexus setup` — this writes an absolute-path MCP config that bypasses `npx` entirely. The pinned-`npx` snippets below are a quickstart fallback; on a cold cache the `npx` install can exceed Claude Code's `MCP_TIMEOUT` default (~30s).

**Claude Code** (full support — MCP + skills + hooks):

```bash
# macOS / Linux
claude mcp add gitnexus -- npx -y gitnexus@latest mcp

# Windows
claude mcp add gitnexus -- cmd /c npx -y gitnexus@latest mcp
```

**Codex** (full support — MCP + skills):

```bash
codex mcp add gitnexus -- npx -y gitnexus@latest mcp
```

**Cursor** (`~/.cursor/mcp.json` — global, works for all projects):

```json
{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}
```

**Antigravity** (Google) — `~/.gemini/antigravity/mcp_config.json`:

```json
{
  "mcpServers": {
    "gitnexus": {
      "command": "npx",
      "args": ["-y", "gitnexus@latest", "mcp"]
    }
  }
}
```

> `gitnexus setup` also merges an `AfterTool` entry into `~/.gemini/settings.json` (under the canonical [Gemini CLI hooks schema](https://geminicli.com/docs/hooks/reference/)) and installs skills to `~/.gemini/antigravity/skills/`. Existing user hooks are preserved. The hook adapter's path is rewritten at install time, so run `gitnexus setup` rather than hand-editing.

**OpenCode** (`~/.config/opencode/config.json`):

```json
{
  "mcp": {
    "gitnexus": {
      "type": "local",
      "command": ["gitnexus", "mcp"]
    }
  }
}
```

**Codex** (`~/.codex/config.toml` for system scope, or `.codex/config.toml` for project scope):

```toml
[mcp_servers.gitnexus]
command = "npx"
args = ["-y", "gitnexus@latest", "mcp"]
```

### CLI Commands

```bash
gitnexus setup                   # Configure MCP for your editors (one-time)
gitnexus analyze [path]          # Index a repository (or update stale index)
gitnexus analyze --repair-fts    # Fast path: rebuild/verify only FTS indexes on existing index data
gitnexus analyze --force         # Full rebuild: re-parse + graph rebuild + FTS rebuild
gitnexus analyze --skills        # Generate repo-specific skill files from detected communities
gitnexus analyze --skip-embeddings  # Skip embedding generation (faster)
gitnexus analyze --skip-agents-md  # Preserve custom AGENTS.md/CLAUDE.md gitnexus section edits
gitnexus analyze --skip-skills     # Skip installing .claude/skills/gitnexus/ skill files
gitnexus analyze --default-branch develop  # Branch used in the generated regression-compare example (base_ref)
gitnexus analyze --skip-git        # Index folders that are not Git repositories
gitnexus analyze --embeddings [limit]  # Enable embedding generation (slower, better search)
gitnexus analyze --verbose       # Log skipped files when parsers are unavailable
gitnexus analyze --worker-timeout 60  # Increase worker idle timeout for slow parses
gitnexus analyze --wal-checkpoint-threshold 67108864  # 64 MiB. Control LadybugDB WAL auto-checkpoint threshold (default: 67108864 = 64 MiB; -1 keeps Ladybug stock ~16 MiB)
gitnexus analyze --workers <n>        # Parse worker pool size (>=1; default: cores-1, capped at 16, auto-sized to the repo). 0 is rejected — there is no sequential mode.
gitnexus mcp                     # Start MCP server (stdio) — serves all indexed repos
gitnexus serve                   # Start local HTTP server (multi-repo) for web UI connection
gitnexus list                    # List all indexed repositories
gitnexus status                  # Show index status for current repo
gitnexus clean                   # Delete index for current repo
gitnexus clean --all --force     # Delete all indexes
gitnexus wiki [path]             # Generate repository wiki from knowledge graph
gitnexus wiki --model <model>    # Wiki with custom LLM model (default: gpt-4o-mini)
gitnexus wiki --base-url <url>   # Wiki with custom LLM API base URL
gitnexus publish                 # Notify the understand-quickly registry (opt-in, see below)

# Repository groups (multi-repo / monorepo service tracking)
gitnexus group create <name>                                   # Create a repository group
gitnexus group add <group> <groupPath> <registryName>          # Add a repo to a group. <groupPath> is a hierarchy path (e.g. hr/hiring/backend); <registryName> is the repo's name from the registry (see `gitnexus list`)
gitnexus group remove <group> <groupPath>                      # Remove a repo from a group by its hierarchy path
gitnexus group list [name]                                     # List groups, or show one group's config
gitnexus group sync <name>                                     # Extract contracts and match across repos/services
gitnexus group contracts <name>  # Inspect extracted contracts and cross-links
gitnexus group query <name> <q>  # Search execution flows across all repos in a group
gitnexus group status <name>     # Check staleness of repos in a group
```

If `analyze` reports a worker parse timeout on a large or unusual repository, it keeps running and falls back safely. To give slow worker jobs more time, use `gitnexus analyze --worker-timeout 60` or set `GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS=60000`. For very large files, `GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES` controls the worker job byte budget.

#### Embeddings node limit

`gitnexus analyze --embeddings` generates semantic search vectors with a default 50,000-node safety cap to protect memory on large repositories. Override the cap when you know the host has enough memory for a larger graph, or disable it entirely for a one-off full embeddings run.

```bash
# Generate embeddings with the default 50,000 node safety cap
gitnexus analyze --embeddings

# Disable the safety cap entirely
gitnexus analyze --embeddings 0

# Use a custom cap
gitnexus analyze --embeddings 100000
```

If embeddings are skipped on a large repository, the indexed graph likely exceeds the default safety cap. Re-run with `gitnexus analyze --embeddings 0` to remove the cap, or `gitnexus analyze --embeddings <n>` to choose a higher limit while still keeping memory bounded.

#### Project config (`.gitnexusrc`)

Commit a `.gitnexusrc` JSON file at the repo root to preconfigure recurring `analyze` options per project, instead of re-passing the same flags every run. It is read from the resolved repo root (not `.gitnexus/`, which is gitignored index storage). **CLI flags always override `.gitnexusrc`.**

```jsonc
{
  // Default branch used in the generated regression-compare example (base_ref).
  // Use this so a project on `develop`/`master` doesn't get "main" rewritten
  // over its fix on every analyze. (Alias: "branch".)
  "defaultBranch": "develop",
  "skipContextFiles": true, // alias of skipAgentsMd: keep your own AGENTS.md/CLAUDE.md
  "skipSkills": true, // don't install .claude/skills/gitnexus/
  "embeddings": true, // generate embeddings by default
  "workerTimeout": 60
}
```

A nested `analyze` block is also accepted (and overrides flat keys for the same option):

```json
{ "analyze": { "defaultBranch": "develop", "skipSkills": true } }
```

Notes:

- The default branch is resolved as: `--default-branch` > `.gitnexusrc` `defaultBranch`/`branch` > auto-detected `origin/HEAD` > `main`.
- `skipContextFiles` / `skipAiContext` are aliases for `skipAgentsMd` — they skip the `AGENTS.md` / `CLAUDE.md` block only. They do **not** imply `skipSkills`. `indexOnly` is the stronger option that skips all file injection.
- Supported keys: `defaultBranch` (`branch`), `skipAgentsMd` (`skipContextFiles`, `skipAiContext`), `skipSkills`, `indexOnly`, `stats`/`noStats`, `embeddings`, `dropEmbeddings`, `name`, `allowDuplicateName`, `maxFileSize`, `workerTimeout`, `walCheckpointThreshold`, `workers`, `embeddingThreads`, `embeddingBatchSize`, `embeddingSubBatchSize`, `embeddingDevice`.
- The file is JSON only. Unknown keys and invalid values fail fast with an actionable error before analysis starts.

#### Environment variables

Most `analyze` knobs are also CLI flags (`--workers`, `--worker-timeout`, `--max-file-size`, `--verbose`). Use the env-var form when you'd otherwise repeat the same flag every run, or when invoking GitNexus from a long-running host (MCP server, eval-server, CI shell) that already manages its own environment. CLI flags take precedence over env vars; env vars take precedence over built-in defaults.

| Variable                               | Default                   | Effect                                                                                                                                                     | Tune when…                                                                                                                                  |
| -------------------------------------- | ------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------- |
| `GITNEXUS_WORKER_POOL_SIZE`            | `cores - 1`, capped at 16 | Parse worker pool size (must be ≥ 1). Equivalent to `--workers <n>`. The worker pool is the sole parse path — there is no sequential parser, so `0` is rejected with an actionable error (the pool self-heals via quarantine + respawn). | Constrained containers (cgroup CPU limits) or CI runners with explicit quotas. To narrow down a worker crash set `1` for a single-worker pool — not `0`. |
| `GITNEXUS_PARSE_CHUNK_CONCURRENCY`     | `2`                       | Number of chunks whose file contents may be read into memory in parallel while the pool dispatches the current chunk. Worker dispatch itself stays serial. | Repos large enough to chunk (multi-MB total source) where disk I/O is a measurable fraction of analyze wall-clock.                          |
| `GITNEXUS_VERBOSE`                     | unset                     | When `1`, enables verbose ingestion logs (skipped-file warnings, per-chunk throughput, parse-cache stats). Equivalent to `--verbose`.                      | Debugging an analyze that "completed" but seems to have missed files; tuning `--workers` / chunk concurrency against observable throughput. |
| `GITNEXUS_PROFILE_DEFERRED`            | unset                     | When `1`, emits `[deferred-profile]` timing/progress logs for the post-chunk deferred resolution band (imports → heritage → buildHeritageMap → legacy call resolution). Implied by `GITNEXUS_VERBOSE`. | Diagnosing analyze stalls in "Resolving calls (all chunks)" on large Java/Kotlin repos (issue #1741) without the full verbose ingestion noise. |
| `GITNEXUS_PROFILE_DEFERRED_SLOW_MS`    | `3000` (verbose) / `5000` | Per-file threshold in ms above which `processCallsFromExtracted` emits a `slow file …` log line. Parsed via `Number()`: accepts integers (`5000`), scientific notation (`2.5e3`), decimals (`.5`), and hex (`0x10`). Non-finite or non-positive values fall back to the default. | Hunting a few outlier files dominating the deferred call-resolution stage; lower to surface more, raise to focus only on the worst.          |
| `GITNEXUS_MAX_FILE_SIZE`               | `512` (KB)                | Walker skip threshold in KB. Hard cap is `32768` (tree-sitter buffer ceiling). Equivalent to `--max-file-size <kb>`.                                       | Indexing repos with intentionally-large source files (generated parsers, vendored bundles) that should still be parsed.                     |
| `GITNEXUS_WORKER_SUB_BATCH_TIMEOUT_MS` | `30000`                   | Worker idle timeout in milliseconds before retry/fallback. Equivalent to `--worker-timeout <seconds>` × 1000.                                              | Slow-parsing files (large minified JS, deeply-nested TS types) that legitimately need more than 30s.                                        |
| `GITNEXUS_WAL_CHECKPOINT_THRESHOLD`       | `67108864` (64 MiB)       | LadybugDB WAL auto-checkpoint threshold in bytes. Equivalent to `--wal-checkpoint-threshold <bytes>`. `-1` keeps LadybugDB's stock threshold (~16 MiB). Larger thresholds reduce checkpoint frequency but increase the WAL size at rotation time — choose a smaller value on disk-constrained environments. | You need a larger or smaller WAL auto-checkpoint threshold for your analyze workload.                                                         |
| `GITNEXUS_WORKER_SUB_BATCH_MAX_BYTES`  | `8388608` (8 MB)          | Per-job byte budget the pool will send to a worker in one `postMessage`.                                                                                   | Very large individual files; mostly diagnostic — bumping past 8 MB risks structured-clone memory pressure.                                  |
| `GITNEXUS_WORKER_MAX_RESPAWNS_PER_SLOT`        | `3`                       | Max replacement spawns per worker slot before the slot is dropped from the active rotation. Bounds respawn loops on a chronically-crashing slot.           | Hosts where a flaky worker should retry more (raise) or fail-fast (lower) before the slot is dropped.                                       |
| `GITNEXUS_WORKER_MAX_CUMULATIVE_TIMEOUT_MS`    | `5 × subBatchTimeoutMs`   | Total retry wall-time budget per job before quarantining. Combined with `timeoutBackoffFactor`, prevents exponentially-growing retries from stalling for hours. | Slow files that legitimately need long total retry windows; lower to fail-fast on stalls.                                                    |
| `GITNEXUS_WORKER_CONSECUTIVE_FAILURE_THRESHOLD`| `max(3, poolSize)`        | Per-slot consecutive deaths before the pool's circuit breaker trips. After tripping, every subsequent dispatch rejects until a fresh pool is created.       | Hosts where a SIGSEGV-prone native grammar should trip the breaker sooner; CI runners that should fail loudly.                              |
| `GITNEXUS_CHUNK_BYTE_BUDGET`           | `2097152` (2 MB)          | Chunk boundary used for cache-key composition and dispatch. Smaller = finer-grained cache hits but more dispatch overhead.                                 | Tuning incremental-analyze cache behavior on monorepos.                                                                                     |
| `GITNEXUS_NO_GITIGNORE`                | unset                     | When set, skips `.gitignore` parsing. `.gitnexusignore` is still honored.                                                                                  | Indexing a repo whose `.gitignore` excludes files you actually want indexed (e.g., generated code committed for cross-repo lookup).         |
| `GITNEXUS_SKIP_OPTIONAL_GRAMMARS`      | unset                     | When `=1` strictly, skips vendored grammar materialize/build for `tree-sitter-dart`, `tree-sitter-proto`, and `tree-sitter-swift` at install time.        | Installing on a host without a C++ toolchain or where Swift prebuilds don't match; you're willing to skip Dart/Proto/Swift parsing.         |

#### Publishing to understand-quickly (opt-in)

[`looptech-ai/understand-quickly`](https://github.com/looptech-ai/understand-quickly) is a public registry of code-knowledge graphs that lists `gitnexus@1` as a first-class format. After registering your repo once (`npx @understand-quickly/cli add` or the [wizard](https://looptech-ai.github.io/understand-quickly/add.html)), `gitnexus publish` fires a single `repository_dispatch` event so the registry resyncs your entry on demand instead of waiting for the nightly job.

It is opt-in and a no-op without `UNDERSTAND_QUICKLY_TOKEN` — a fine-grained GitHub PAT with `Repository dispatches: write` on the registry repo. Nothing else happens; no graph file is uploaded. See the [protocol spec](https://github.com/looptech-ai/understand-quickly/blob/main/docs/integrations/protocol.md) for the full contract.

### What Your AI Agent Gets

**16 tools** exposed via MCP (11 per-repo + 5 group):

| Tool              | What It Does                                                     | `repo` Param |
| ----------------- | ---------------------------------------------------------------- | ------------ |
| `list_repos`      | Discover all indexed repositories                                | —            |
| `query`           | Process-grouped hybrid search (BM25 + semantic + RRF)            | Optional     |
| `context`         | 360-degree symbol view — categorized refs, process participation | Optional     |
| `impact`          | Blast radius analysis with depth grouping and confidence         | Optional     |
| `detect_changes`  | Git-diff impact — maps changed lines to affected processes       | Optional     |
| `rename`          | Multi-file coordinated rename with graph + text search           | Optional     |
| `cypher`          | Raw Cypher graph queries                                         | Optional     |
| `group_list`      | List configured repository groups                                | —            |
| `group_sync`      | Extract contracts and match across repos/services                | —            |
| `group_contracts` | Inspect extracted contracts and cross-links                      | —            |
| `group_query`     | Search execution flows across all repos in a group               | —            |
| `group_status`    | Check staleness of repos in a group                              | —            |

> When only one repo is indexed, the `repo` parameter is optional. With multiple repos, specify which one: `query({query: "auth", repo: "my-app"})`.

**Resources** for instant context:

| Resource                                | Purpose                                              |
| --------------------------------------- | ---------------------------------------------------- |
| `gitnexus://repos`                      | List all indexed repositories (read this first)      |
| `gitnexus://repo/{name}/context`        | Codebase stats, staleness check, and available tools |
| `gitnexus://repo/{name}/clusters`       | All functional clusters with cohesion scores         |
| `gitnexus://repo/{name}/cluster/{name}` | Cluster members and details                          |
| `gitnexus://repo/{name}/processes`      | All execution flows                                  |
| `gitnexus://repo/{name}/process/{name}` | Full process trace with steps                        |
| `gitnexus://repo/{name}/schema`         | Graph schema for Cypher queries                      |

**2 MCP prompts** for guided workflows:

| Prompt          | What It Does                                                              |
| --------------- | ------------------------------------------------------------------------- |
| `detect_impact` | Pre-commit change analysis — scope, affected processes, risk level        |
| `generate_map`  | Architecture documentation from the knowledge graph with mermaid diagrams |

**4 agent skills** installed to `.claude/skills/` automatically:

- **Exploring** — Navigate unfamiliar code using the knowledge graph
- **Debugging** — Trace bugs through call chains
- **Impact Analysis** — Analyze blast radius before changes
- **Refactoring** — Plan safe refactors using dependency mapping

**Repo-specific skills** generated with `--skills`:

When you run `gitnexus analyze --skills`, GitNexus detects the functional areas of your codebase (via Leiden community detection) and generates a `SKILL.md` file for each one under `.claude/skills/generated/`. Each skill describes a module's key files, entry points, execution flows, and cross-area connections — so your AI agent gets targeted context for the exact area of code you're working in. Skills are regenerated on each `--skills` run to stay current with the codebase.

---

## Multi-Repo MCP Architecture

GitNexus uses a **global registry** so one MCP server can serve multiple indexed repos. No per-project MCP config needed — set it up once and it works everywhere.

```mermaid
flowchart TD
    subgraph CLI [CLI Commands]
        Setup["gitnexus setup"]
        Analyze["gitnexus analyze"]
        Clean["gitnexus clean"]
        List["gitnexus list"]
    end

    subgraph Registry ["~/.gitnexus/"]
        RegFile["registry.json"]
    end

    subgraph Repos [Project Repos]
        RepoA[".gitnexus/ in repo A"]
        RepoB[".gitnexus/ in repo B"]
    end

    subgraph MCP [MCP Server]
        Server["server.ts"]
        Backend["LocalBackend"]
        Pool["Connection Pool"]
        ConnA["LadybugDB conn A"]
        ConnB["LadybugDB conn B"]
    end

    Setup -->|"writes global MCP config"| CursorConfig["~/.cursor/mcp.json"]
    Analyze -->|"registers repo"| RegFile
    Analyze -->|"stores index"| RepoA
    Clean -->|"unregisters repo"| RegFile
    List -->|"reads"| RegFile
    Server -->|"reads registry"| RegFile
    Server --> Backend
    Backend --> Pool
    Pool -->|"lazy open"| ConnA
    Pool -->|"lazy open"| ConnB
    ConnA -->|"queries"| RepoA
    ConnB -->|"queries"| RepoB
```

**How it works:** Each `gitnexus analyze` stores the index in `.gitnexus/` inside the repo (portable, gitignored) and registers a pointer in `~/.gitnexus/registry.json`. When an AI agent starts, the MCP server reads the registry and can serve any indexed repo. LadybugDB connections are opened lazily on first query and evicted after 5 minutes of inactivity (max 5 concurrent). If only one repo is indexed, the `repo` parameter is optional on all tools — agents don't need to change anything.

---

## Web UI (browser-based)

A client-side graph explorer and AI chat — your code never leaves your machine.

**Try it now:** [gitnexus.vercel.app](https://gitnexus.vercel.app) — run `npx gitnexus@latest serve` locally and the page auto-connects to your local backend.

<img width="2550" height="1343" alt="gitnexus_img" src="https://github.com/user-attachments/assets/cc5d637d-e0e5-48e6-93ff-5bcfdb929285" />

Or run the frontend locally:

```bash
git clone https://github.com/abhigyanpatwari/gitnexus.git
cd gitnexus/gitnexus-shared && npm install && npm run build
cd ../gitnexus-web && npm install
npm run dev
# Then in another terminal, start the backend the frontend connects to:
npx gitnexus@latest serve
```

## Docker

The official Docker setup ships **two signed images** orchestrated by `docker-compose.yaml`. Each image is published to both **GitHub Container Registry** (GHCR) and **Docker Hub** — same build, same digest, same Cosign signature — so pick whichever registry you prefer:

| Purpose                                                                | GHCR (default in `docker-compose.yaml`)       | Docker Hub mirror              |
| ---------------------------------------------------------------------- | --------------------------------------------- | ------------------------------ |
| CLI / `gitnexus serve` backend (HTTP API on port `4747`, MCP, indexer) | `ghcr.io/abhigyanpatwari/gitnexus:latest`     | `akonlabs/gitnexus:latest`     |
| Static web UI (port `4173`)                                            | `ghcr.io/abhigyanpatwari/gitnexus-web:latest` | `akonlabs/gitnexus-web:latest` |

> **Heads-up — image rename.** Earlier releases published the web UI under
> `ghcr.io/abhigyanpatwari/gitnexus`. Starting with the introduction of the
> bundled backend, that slug now hosts the CLI/server image and the UI moved
> to `ghcr.io/abhigyanpatwari/gitnexus-web`. The previous tags remain
> available for pulling, but new versions are only published under the new
> slugs. Update your `docker run` / compose files accordingly (or just adopt
> the bundled compose).

### One-command setup

```bash
docker compose up -d
```

This starts the server on `http://localhost:4747` and the web UI on
`http://localhost:4173`. The UI auto-detects the server because the browser
runs on the host and reaches the container via the mapped port.

A named volume (`gitnexus-data`) persists the global registry, indexes, and
cloned repos at `/data/gitnexus` inside the server container. To make repos on
your host machine indexable, set `WORKSPACE_DIR` before bringing the stack up:

```bash
WORKSPACE_DIR=$HOME/code docker compose up -d
# Inside the server container the directory is mounted read-only at /workspace.
docker compose exec gitnexus-server gitnexus index /workspace/my-repo
```

### Direct `docker run`

```bash
# Server
docker run --rm -d \
  --name gitnexus-server \
  -p 4747:4747 \
  -v gitnexus-data:/data/gitnexus \
  ghcr.io/abhigyanpatwari/gitnexus:latest

# Web UI
docker run --rm -d \
  --name gitnexus-web \
  -p 4173:4173 \
  ghcr.io/abhigyanpatwari/gitnexus-web:latest
```

Optional env file (override image tags, container names, ports, workspace dir):

```bash
cp .env.example .env
docker compose --env-file .env up -d
```

### Versioning & supply-chain protection

The Docker images are version-locked to the npm package:

- Stable images are **only published from `vX.Y.Z` git tags** (via `docker.yml`
  triggered directly by the tag push), and the workflow refuses to build unless
  the tag exactly matches `gitnexus/package.json`'s version. So
  `ghcr.io/abhigyanpatwari/gitnexus:1.6.2` (and its Docker Hub mirror
  `akonlabs/gitnexus:1.6.2`) is byte-for-byte the same release as
  `npm install gitnexus@1.6.2` — no drift, no floating builds from `main`.
  Both registries receive the same digest from a single build step, so you can
  pull from either and the signature verifies identically.
- Release-candidate images (e.g. `:1.7.0-rc.1`) are published alongside each
  RC npm release. They are built by `publish.yml` calling `docker.yml`
  as a reusable workflow after the RC tag is created and pushed.
- `:latest` is auto-promoted only from non-prerelease tags by the Docker
  metadata action, so it always points at a real, npm-published version.

Both images are signed with [Cosign keyless signing][cosign-keyless] using the
workflow's GitHub OIDC identity, and shipped with build provenance and SBOM
attestations. **This is your protection against supply-chain attacks**: even if
an attacker republishes a same-named image elsewhere (or somehow pushes to a
typo-squatted registry), they cannot forge a Cosign signature tied to
`abhigyanpatwari/GitNexus`'s `docker.yml`. Always verify before pulling into
sensitive environments:

**Stable releases** — signed from the `v*` tag ref:

```bash
cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
  --certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com

# Same signature verifies the Docker Hub mirror (identical digest):
cosign verify docker.io/akonlabs/gitnexus:1.6.2 \
  --certificate-identity-regexp '^https://github\.com/abhigyanpatwari/GitNexus/\.github/workflows/docker\.yml@refs/tags/v[0-9]+\.[0-9]+\.[0-9]+(-[a-zA-Z0-9.]+)?$' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com
```

The regex pins the certificate identity to this repo's `docker.yml` workflow
**run from a `v*` tag** — rejecting unsigned images, images signed by other
workflows, and images signed from unprotected refs. It is identical for both
registries because both sets of tags were signed at the same digest in one
workflow run.

**Release candidates** — signed from `refs/heads/main` (the caller's ref when
`publish.yml` invokes `docker.yml` as a reusable workflow):

```bash
cosign verify ghcr.io/abhigyanpatwari/gitnexus:1.7.0-rc.1 \
  --certificate-identity 'https://github.com/abhigyanpatwari/GitNexus/.github/workflows/docker.yml@refs/heads/main' \
  --certificate-oidc-issuer https://token.actions.githubusercontent.com
```

You can also inspect the build provenance and SBOM:

```bash
cosign download attestation ghcr.io/abhigyanpatwari/gitnexus:1.6.2 \
  --predicate-type https://slsa.dev/provenance/v1
```

#### Kubernetes: enforce signatures at admission

For Kubernetes deployments, ship the bundled
[`ClusterImagePolicy`](deploy/kubernetes/cluster-image-policy.yaml) so the
[Sigstore policy-controller][policy-controller] rejects any GitNexus pod whose
image is not signed by this repo's `docker.yml` running from a `vX.Y.Z` tag —
the same identity the `cosign verify` snippet above pins.

```bash
# 1. Install the controller (one-time, cluster-wide)
helm repo add sigstore https://sigstore.github.io/helm-charts && helm repo update
helm install policy-controller -n cosign-system --create-namespace \
  sigstore/policy-controller

# 2. Opt your namespace in
kubectl label namespace <your-ns> policy.sigstore.dev/include=true

# 3. Apply the policy
kubectl apply -f deploy/kubernetes/cluster-image-policy.yaml
```

After this, attempting to deploy an unsigned image — or one signed by anything
other than `abhigyanpatwari/GitNexus`'s `docker.yml` at a `v*` tag — fails the
admission webhook before a pod is ever created. This turns the verifiable
signature into an enforced policy, which is the supply-chain control most
clusters actually need.

[cosign-keyless]: https://docs.sigstore.dev/cosign/signing/overview/
[policy-controller]: https://docs.sigstore.dev/policy-controller/overview/

### Files

- [Dockerfile.web](Dockerfile.web) — builds `gitnexus-shared` and `gitnexus-web`, then serves the production frontend.
- [Dockerfile.cli](Dockerfile.cli) — builds the CLI/server (with its native deps) and runs `gitnexus serve --host 0.0.0.0`.
- [docker-compose.yaml](docker-compose.yaml) — starts both signed images side by side.
- [.env.example](.env.example) — overrides for image names, container names, ports, and the workspace mount.

The web UI uses the same indexing pipeline as the CLI but runs entirely in WebAssembly (Tree-sitter WASM, LadybugDB WASM, in-browser embeddings). It's great for quick exploration but limited by browser memory for larger repos.

**Local Backend Mode:** Run `gitnexus serve` and open the web UI locally — it auto-detects the server and shows all your indexed repos, with full AI chat support. No need to re-upload or re-index. The agent's tools (Cypher queries, search, code navigation) route through the backend HTTP API automatically.

---

## The Problem GitNexus Solves

Tools like **Cursor**, **Claude Code**, **Codex**, **Cline**, **Roo Code**, and **Windsurf** are powerful — but they don't truly know your codebase structure.

**What happens:**

1. AI edits `UserService.validate()`
2. Doesn't know 47 functions depend on its return type
3. **Breaking changes ship**

### Traditional Graph RAG vs GitNexus

Traditional approaches give the LLM raw graph edges and hope it explores enough. GitNexus **precomputes structure at index time** — clustering, tracing, scoring — so tools return complete context in one call:

```mermaid
flowchart TB
    subgraph Traditional["Traditional Graph RAG"]
        direction TB
        U1["User: What depends on UserService?"]
        U1 --> LLM1["LLM receives raw graph"]
        LLM1 --> Q1["Query 1: Find callers"]
        Q1 --> Q2["Query 2: What files?"]
        Q2 --> Q3["Query 3: Filter tests?"]
        Q3 --> Q4["Query 4: High-risk?"]
        Q4 --> OUT1["Answer after 4+ queries"]
    end

    subgraph GN["GitNexus Smart Tools"]
        direction TB
        U2["User: What depends on UserService?"]
        U2 --> TOOL["impact UserService upstream"]
        TOOL --> PRECOMP["Pre-structured response:
        8 callers, 3 clusters, all 90%+ confidence"]
        PRECOMP --> OUT2["Complete answer, 1 query"]
    end
```

**Core innovation: Precomputed Relational Intelligence**

- **Reliability** — LLM can't miss context, it's already in the tool response
- **Token efficiency** — No 10-query chains to understand one function
- **Model democratization** — Smaller LLMs work because tools do the heavy lifting

---

## How It Works

GitNexus builds a complete knowledge graph of your codebase through a multi-phase indexing pipeline:

1. **Structure** — Walks the file tree and maps folder/file relationships
2. **Parsing** — Extracts functions, classes, methods, and interfaces using Tree-sitter ASTs
3. **Resolution** — Resolves imports, function calls, heritage, constructor inference, and `self`/`this` receiver types across files with language-aware logic
4. **Clustering** — Groups related symbols into functional communities
5. **Processes** — Traces execution flows from entry points through call chains
6. **Search** — Builds hybrid search indexes for fast retrieval

### Supported Languages

| Language   | Imports | Named Bindings | Exports | Heritage | Type Annotations | Constructor Inference | Config | Frameworks | Entry Points |
| ---------- | ------- | -------------- | ------- | -------- | ---------------- | --------------------- | ------ | ---------- | ------------ |
| TypeScript | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| JavaScript | ✓       | ✓              | ✓       | ✓        | —                | ✓                     | ✓      | ✓          | ✓            |
| Python     | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| Java       | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
| Kotlin     | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
| C#         | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| Go         | ✓       | —              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| Rust       | ✓       | ✓              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
| PHP        | ✓       | ✓              | ✓       | —        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| Ruby       | ✓       | —              | ✓       | ✓        | —                | ✓                     | —      | ✓          | ✓            |
| Swift      | —       | —              | ✓       | ✓        | ✓                | ✓                     | ✓      | ✓          | ✓            |
| C          | —       | —              | ✓       | —        | ✓                | ✓                     | —      | ✓          | ✓            |
| C++        | —       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |
| Dart       | ✓       | —              | ✓       | ✓        | ✓                | ✓                     | —      | ✓          | ✓            |

**Imports** — cross-file import resolution · **Named Bindings** — `import { X as Y }` / re-export tracking · **Exports** — public/exported symbol detection · **Heritage** — class inheritance, interfaces, mixins · **Type Annotations** — explicit type extraction for receiver resolution · **Constructor Inference** — infer receiver type from constructor calls (`self`/`this` resolution included for all languages) · **Config** — language toolchain config parsing (tsconfig, go.mod, etc.) · **Frameworks** — AST-based framework pattern detection · **Entry Points** — entry point scoring heuristics

---

## Tool Examples

### Impact Analysis

```
impact({target: "UserService", direction: "upstream", minConfidence: 0.8})

TARGET: Class UserService (src/services/user.ts)

UPSTREAM (what depends on this):
  Depth 1 (WILL BREAK):
    handleLogin [CALLS 90%] -> src/api/auth.ts:45
    handleRegister [CALLS 90%] -> src/api/auth.ts:78
    UserController [CALLS 85%] -> src/controllers/user.ts:12
  Depth 2 (LIKELY AFFECTED):
    authRouter [IMPORTS] -> src/routes/auth.ts
```

Options: `maxDepth`, `minConfidence`, `relationTypes` (`CALLS`, `IMPORTS`, `EXTENDS`, `IMPLEMENTS`), `includeTests`, `limit` (max symbols per depth, default 100), `offset` (pagination start per depth), `summaryOnly` (counts and risk only, omits symbol list)

**Disambiguation** — when several symbols share the target name, `impact` returns a ranked `ambiguous` candidate list instead of guessing. Narrow it with `target_uid` (exact, zero-ambiguity), `file_path`, or `kind` (`Function`, `Class`, `Method`, …). From the CLI these are `--uid`, `--file`, and `--kind`, matching `gitnexus context`:

```bash
gitnexus impact get_embeddings                       # → ambiguous: lists ranked candidates
gitnexus impact get_embeddings --file src/embed.py   # → resolves to the one in that file
gitnexus impact get_embeddings --uid "Function:src/embed.py:get_embeddings"  # exact
```

### Process-Grouped Search

```
query({query: "authentication middleware"})

processes:
  - summary: "LoginFlow"
    priority: 0.042
    symbol_count: 4
    process_type: cross_community
    step_count: 7

process_symbols:
  - name: validateUser
    type: Function
    filePath: src/auth/validate.ts
    process_id: proc_login
    step_index: 2

definitions:
  - name: AuthConfig
    type: Interface
    filePath: src/types/auth.ts
```

### Context (360-degree Symbol View)

```
context({name: "validateUser"})

symbol:
  uid: "Function:validateUser"
  kind: Function
  filePath: src/auth/validate.ts
  startLine: 15

incoming:
  calls: [handleLogin, handleRegister, UserController]
  imports: [authRouter]

outgoing:
  calls: [checkPassword, createSession]

processes:
  - name: LoginFlow (step 2/7)
  - name: RegistrationFlow (step 3/5)
```

### Detect Changes (Pre-Commit)

```
detect_changes({scope: "all"})

summary:
  changed_count: 12
  affected_count: 3
  changed_files: 4
  risk_level: medium

changed_symbols: [validateUser, AuthService, ...]
affected_processes: [LoginFlow, RegistrationFlow, ...]
```

### Rename (Multi-File)

```
rename({symbol_name: "validateUser", new_name: "verifyUser", dry_run: true})

status: success
files_affected: 5
total_edits: 8
graph_edits: 6     (high confidence)
text_search_edits: 2  (review carefully)
changes: [...]
```

### Cypher Queries

```cypher
-- Find what calls auth functions with high confidence
MATCH (c:Community {heuristicLabel: 'Authentication'})<-[:CodeRelation {type: 'MEMBER_OF'}]-(fn)
MATCH (caller)-[r:CodeRelation {type: 'CALLS'}]->(fn)
WHERE r.confidence > 0.8
RETURN caller.name, fn.name, r.confidence
ORDER BY r.confidence DESC
```

---

## Wiki Generation

Generate LLM-powered documentation from your knowledge graph:

```bash
# Requires an LLM API key (OPENAI_API_KEY, etc.)
gitnexus wiki

# Use a custom model or provider
gitnexus wiki --model gpt-4o
gitnexus wiki --base-url https://api.anthropic.com/v1

# Force full regeneration
gitnexus wiki --force


# Increase the timeout or retries for large codebase or slow LLM providers
gitnexus wiki --timeout <seconds> # LLM request timeout in seconds (default: disabled)
gitnexus wiki --retries <n>      # Max LLM retry attempts per request (default: 3)

# Change the language generation for wiki
gitnexus wiki --lang <lang>  # Output language for generated documentation (e.g. english, chinese, spanish, japanese)
```

The wiki generator reads the indexed graph structure, groups files into modules via LLM, generates per-module documentation pages, and creates an overview page — all with cross-references to the knowledge graph.

---

## Tech Stack

| Layer               | CLI                                   | Web                                     |
| ------------------- | ------------------------------------- | --------------------------------------- |
| **Runtime**         | Node.js (native)                      | Browser (WASM)                          |
| **Parsing**         | Tree-sitter native bindings           | Tree-sitter WASM                        |
| **Database**        | LadybugDB native                      | LadybugDB WASM                          |
| **Embeddings**      | HuggingFace transformers.js (GPU/CPU) | transformers.js (WebGPU/WASM)           |
| **Search**          | BM25 + semantic + RRF                 | BM25 + semantic + RRF                   |
| **Agent Interface** | MCP (stdio)                           | LangChain ReAct agent                   |
| **Visualization**   | —                                     | Sigma.js + Graphology (WebGL)           |
| **Frontend**        | —                                     | React 18, TypeScript, Vite, Tailwind v4 |
| **Clustering**      | Graphology                            | Graphology                              |
| **Concurrency**     | Worker threads + async                | Web Workers + Comlink                   |

---

## Roadmap

### Actively Building

- [ ] **LLM Cluster Enrichment** — Semantic cluster names via LLM API
- [ ] **AST Decorator Detection** — Parse @Controller, @Get, etc.
- [ ] **Incremental Indexing** — Only re-index changed files

### Recently Completed

- [x] Constructor-Inferred Type Resolution, `self`/`this` Receiver Mapping
- [x] Wiki Generation, Multi-File Rename, Git-Diff Impact Analysis
- [x] Process-Grouped Search, 360-Degree Context, Claude Code Hooks
- [x] Multi-Repo MCP, Zero-Config Setup, 14 Language Support
- [x] Community Detection, Process Detection, Confidence Scoring
- [x] Hybrid Search, Vector Index

---

## Security & Privacy

- **CLI**: Everything runs locally on your machine. No network calls. Index stored in `.gitnexus/` (gitignored). Global registry at `~/.gitnexus/` stores only paths and metadata.
- **Web**: Everything runs in your browser. No code uploaded to any server. API keys stored in localStorage only.
- Open source — audit the code yourself.

---

## Acknowledgments

- [Tree-sitter](https://tree-sitter.github.io/) — AST parsing
- [LadybugDB](https://ladybugdb.com/) — Embedded graph database with vector support (formerly KuzuDB)
- [Sigma.js](https://www.sigmajs.org/) — WebGL graph rendering
- [transformers.js](https://huggingface.co/docs/transformers.js) — Browser ML
- [Graphology](https://graphology.github.io/) — Graph data structures
- [MCP](https://modelcontextprotocol.io/) — Model Context Protocol
