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

1. Read ontoindex://repo/{name}/context to verify the index loaded
2. 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