gitnexus-cli

# GitNexus CLI Commands

All commands work via `npx` — no global install required.

## Commands

### analyze — Build or refresh the index

```bash
npx gitnexus analyze
```

Run from the project root. This parses all source files, builds the knowledge graph, writes it to `.gitnexus/`, and generates CLAUDE.md / AGENTS.md context files.
| 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. |

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 run `analyze` — the hook does not run analyze itself, to avoid blocking the agent for up to 120s and risking KuzuDB corruption on timeout.

### status — Check index freshness

```bash
npx gitnexus 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
npx gitnexus 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
npx gitnexus 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
npx gitnexus 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