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

# 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:

NODE_OPTIONS="--max-old-space-size=16384" npx gitnexus analyze

Next Steps

Index Repository

Learn how to index your first repository

Setup Editors

Configure MCP for your AI editor

Generate Wiki

Create LLM-powered documentation

Start Server

Run the local HTTP server