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 bunx, else npx), so no package-manager assumption and no global install is required — including on a bun-only machine, which has no npm, npx or pnpm at all.

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)? (Re)generate it with npx gitnexus analyze from the project root, or bunx gitnexus@latest analyze on a bun-only machine. On npm 11.x, if npx crashes during install (node.target is null), install once with npm i -g gitnexus (then gitnexus analyze), or use bunx gitnexus@latest analyze, or pnpm --allow-build=@ladybugdb/core --allow-build=gitnexus --allow-build=tree-sitter dlx gitnexus@latest analyze. See #1939.

Commands

analyze — Build or refresh the index

node .gitnexus/run.cjs 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.
--pdg	Build the program-dependence layers used by explain and pdg_query (taint, CDG, and REACHING_DEF).

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

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-M3)
--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

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