# Gitnexus CLI

> Use when the user needs to run GitNexus CLI commands like analyze/index a repo, check status, clean the index, generate a wiki, or list indexed repos. Examples: "Index this repo", "Reanalyze the codebase", "Generate a wiki"

- Skill: `douglasmonsky/gitnexus-cli` (Agent Skill)
- Install (CLI): `npx skillmds@latest add douglasmonsky/gitnexus-cli`
- Raw SKILL.md: https://api.skillmd.com/api/skills/douglasmonsky/gitnexus-cli/raw
- Safety review: pending (external: skill-scanner PASS, skillspector CAUTION)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: douglasmonsky (https://skillmd.com/u/douglasmonsky)
- Updated: 2026-09-10
- Page: https://skillmd.com/skills/douglasmonsky/gitnexus-cli

---


# GitNexus CLI Commands

Commands below use `node .gitnexus/run.cjs <command>` — the project-local runner `gitnexus analyze` drops next to the index. It auto-selects an available runner at call time (global `gitnexus`, else `pnpm dlx`, else `npx`), so no package-manager assumption and no global install is required.

> **Not analyzed yet, or `node .gitnexus/run.cjs` reports `Cannot find module`** (the gitignored runner is absent — e.g. a fresh clone or `git clean`)? Build only the local index with `npx gitnexus analyze --index-only .` from the project root. On **npm 11.x**, if `npx` crashes during install (`node.target is null`), install once with `npm i -g gitnexus` (then `gitnexus analyze --index-only .`) or use `pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze --index-only .`. See [#1939](https://github.com/abhigyanpatwari/GitNexus/issues/1939).

## Commands

### analyze — Build or refresh the index

```bash
node .gitnexus/run.cjs analyze --index-only .
```

Run from the project root. This parses source files, builds the knowledge graph,
and writes it to `.gitnexus/` without modifying repository guidance.

| Flag                | Effect                                                                                                |
| ------------------- | ----------------------------------------------------------------------------------------------------- |
| `--force`           | Force full re-index even if up to date                                                                |
| `--embeddings`      | Enable embedding generation for semantic search (off by default)                                      |
| `--drop-embeddings` | Drop existing embeddings on rebuild. By default, an `analyze` without `--embeddings` preserves them.  |
| `--pdg`             | Build the program-dependence layers used by `explain` and `pdg_query` (taint, CDG, and REACHING_DEF). |
| `--index-only`      | Refresh only the graph; do not rewrite agent guidance or repo-local skills.                           |

**When to run:** First time in a project, after major code changes, or when
`gitnexus://repo/{name}/context` reports the index is stale. In Claude Code, a
PostToolUse hook detects staleness after `git commit` and `git merge` and
notifies the agent to refresh the index; the hook does not run analysis itself,
to avoid blocking the agent for up to 120s and risking KuzuDB corruption on
timeout.

### Regenerate agent guidance explicitly

Use a full `node .gitnexus/run.cjs analyze .` only when the user explicitly
requests regeneration of `AGENTS.md`, `CLAUDE.md`, or repo-local skills. Review
and normalize those generated changes before committing them.

### status — Check index freshness

```bash
node .gitnexus/run.cjs status
```

Shows whether the current repo has a GitNexus index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.

### clean — Delete the index

```bash
node .gitnexus/run.cjs clean
```

Deletes the `.gitnexus/` directory and unregisters the repo from the global registry. Use before re-indexing if the index is corrupt or after removing GitNexus from a project.

| Flag      | Effect                                            |
| --------- | ------------------------------------------------- |
| `--force` | Skip confirmation prompt                          |
| `--all`   | Clean all indexed repos, not just the current one |

### wiki — Generate documentation from the graph

```bash
node .gitnexus/run.cjs wiki
```

Generates repository documentation from the knowledge graph using an LLM. Requires an API key (saved to `~/.gitnexus/config.json` on first use).

| Flag                | Effect                                    |
| ------------------- | ----------------------------------------- |
| `--force`           | Force full regeneration                   |
| `--model <model>`   | LLM model (default: minimax/minimax-m2.5) |
| `--base-url <url>`  | LLM API base URL                          |
| `--api-key <key>`   | LLM API key                               |
| `--concurrency <n>` | Parallel LLM calls (default: 3)           |
| `--gist`            | Publish wiki as a public GitHub Gist      |

### list — Show all indexed repos

```bash
node .gitnexus/run.cjs list
```

Lists all repositories registered in `~/.gitnexus/registry.json`. The MCP `list_repos` tool provides the same information.

## After Indexing

1. **Read `gitnexus://repo/{name}/context`** to verify the index loaded
2. Use the other GitNexus skills (`exploring`, `debugging`, `impact-analysis`, `refactoring`) for your task

## Troubleshooting

- **"Not inside a git repository"**: Run from a directory inside a git repo
- **Index is stale after re-analyzing**: Restart Claude Code to reload the MCP server
- **Embeddings slow**: Omit `--embeddings` (it's off by default) or set `OPENAI_API_KEY` for faster API-based embedding