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.…
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)
--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.
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, also required to re-gerenate an existing wiki in a different language
--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
--timeout <seconds>
LLM request timeout in seconds (default: disabled)
--retries <n>
Max LLM retry attempts per request (default: 3)
--lang <lang>
Output language for generated documentation (e.g. english, chinese, spanish, japanese)
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 embeddingdon't have the plugin yet? install it then click "run inline in claude" again.