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.

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.

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).

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

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