> ## Documentation Index
> Fetch the complete documentation index at: https://mintlify.com/abhigyanpatwari/GitNexus/llms.txt
> Use this file to discover all available pages before exploring further.

# CLI Overview

> Command-line interface for indexing and managing repositories with GitNexus

GitNexus provides a powerful command-line interface for indexing repositories, managing the knowledge graph, and serving data to AI tools.

## Quick Start

```bash theme={null}
# Index your repository
npx gitnexus analyze

# Configure MCP for your editor (one-time)
npx gitnexus setup

# Start the local server for web UI
npx gitnexus serve
```

## Available Commands

### Core Commands

| Command          | Description                                                 |
| ---------------- | ----------------------------------------------------------- |
| `analyze [path]` | Index a repository into the knowledge graph                 |
| `setup`          | Configure MCP integration for supported editors             |
| `serve`          | Start local HTTP server for web UI connection               |
| `clean`          | Delete GitNexus index for current or all repos              |
| `wiki [path]`    | Generate LLM-powered documentation from the knowledge graph |

### Repository Management

| Command  | Description                              |
| -------- | ---------------------------------------- |
| `list`   | List all indexed repositories            |
| `status` | Show index status for current repository |

### MCP Server

| Command | Description                                         |
| ------- | --------------------------------------------------- |
| `mcp`   | Start MCP server (stdio) — serves all indexed repos |

### Direct Tool Access

These commands bypass MCP overhead and invoke the knowledge graph directly:

| Command           | Description                                     |
| ----------------- | ----------------------------------------------- |
| `query <search>`  | Search for execution flows related to a concept |
| `context [name]`  | Get 360-degree view of a code symbol            |
| `impact <target>` | Blast radius analysis for a symbol              |
| `cypher <query>`  | Execute raw Cypher queries against the graph    |

### Advanced Commands

| Command             | Description                                                |
| ------------------- | ---------------------------------------------------------- |
| `augment <pattern>` | Augment search patterns with graph context (used by hooks) |
| `eval-server`       | Start HTTP server for benchmark evaluation                 |

## Global vs Repository-Specific

### Global Commands

These commands work from any directory:

* `setup` — Configures MCP globally for all projects
* `list` — Shows all indexed repositories
* `serve` — Serves all indexed repositories
* `mcp` — Serves all indexed repositories via MCP

### Repository-Specific Commands

These commands must be run from within a git repository:

* `analyze` — Indexes the current repository
* `status` — Shows index status for current repository
* `clean` — Removes index for current repository
* `wiki` — Generates documentation for current repository
* `query`, `context`, `impact`, `cypher` — Query the knowledge graph

## Storage Architecture

### Local Repository Storage (`.gitnexus/`)

Each indexed repository gets a `.gitnexus/` directory at its root:

```
my-repo/
├── .gitnexus/
│   ├── db/              # KuzuDB graph database
│   ├── wiki/            # Generated documentation (if using wiki command)
│   └── meta.json        # Index metadata (commit hash, stats, timestamp)
├── AGENTS.md            # Agent context file (auto-generated)
└── CLAUDE.md            # Claude Code context file (auto-generated)
```

The `.gitnexus/` directory is automatically added to `.gitignore`.

### Global Registry (`~/.gitnexus/`)

GitNexus maintains a global registry of all indexed repositories:

```
~/.gitnexus/
├── registry.json        # Paths to all indexed repositories
├── config.json          # CLI configuration (LLM API keys, etc.)
└── skills/              # Global agent skills (if using setup command)
```

**Purpose:**

* MCP server discovers and serves all indexed repos automatically
* Multi-repo workflows without re-indexing
* Centralized configuration for LLM providers

## Command Options

Most commands support:

* `-h, --help` — Show help for the command
* `-V, --version` — Show GitNexus version

## Memory Management

GitNexus automatically allocates up to **8GB of heap memory** for large repositories (e.g., Linux kernel). If you need to customize this:

```bash theme={null}
NODE_OPTIONS="--max-old-space-size=16384" npx gitnexus analyze
```

## Next Steps

<CardGroup cols={2}>
  <Card title="Index Repository" icon="magnifying-glass" href="/cli/analyze">
    Learn how to index your first repository
  </Card>

  <Card title="Setup Editors" icon="wrench" href="/cli/setup">
    Configure MCP for your AI editor
  </Card>

  <Card title="Generate Wiki" icon="book" href="/cli/wiki">
    Create LLM-powered documentation
  </Card>

  <Card title="Start Server" icon="server" href="/cli/serve">
    Run the local HTTP server
  </Card>
</CardGroup>