| name | gitnexus-cli |
| description | 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" |
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.
Commands
analyze — Build or refresh the index
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
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
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
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
node .gitnexus/run.cjs list
Lists all repositories registered in ~/.gitnexus/registry.json. The MCP list_repos tool provides the same information.
After Indexing
- Read
gitnexus://repo/{name}/context to verify the index loaded
- 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
