| name | ontoindex-cli |
| description | Use when the user needs to run OntoIndex 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" |
OntoIndex CLI Commands
All commands work via npx — no global install required.
Commands
analyze — Build or refresh the index
npx ontoindex analyze
Run from the project root. This parses all source files, builds the knowledge graph, writes it to .ontoindex/, 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 ontoindex://repo/{name}/context reports the index is stale. In Claude Code, a PostToolUse hook runs analyze automatically after git commit and git merge, preserving embeddings if previously generated.
status — Check index freshness
npx ontoindex status
Shows whether the current repo has a OntoIndex index, when it was last updated, and symbol/relationship counts. Use this to check if re-indexing is needed.
clean — Delete the index
npx ontoindex clean
Deletes the .ontoindex/ directory and unregisters the repo from the global registry. Use before re-indexing if the index is corrupt or after removing OntoIndex 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 ontoindex wiki
Generates repository documentation from the knowledge graph using an LLM. Requires an API key (saved to ~/.ontoindex/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 ontoindex list
Lists all repositories registered in ~/.ontoindex/registry.json. The MCP list_repos tool provides the same information.
After Indexing
- Read
ontoindex://repo/{name}/context to verify the index loaded
- Use the other OntoIndex 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
