GitNexus CLI Commands

All commands work via npx — no global install required.

Commands

analyze — Build or refresh the index

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)

When to run: First time in a project, after major code changes, or when gitnexus://repo/{name}/context reports the index is stale.

status — Check index freshness

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

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

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

npx gitnexus 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