Skill v1.0.1
currentAutomated scan100/100+4 new
name: ontoindex-cli description: 'Use when the user needs to operate the OntoIndex CLI to index, inspect, clean, or document a repository.' metadata: version: "1.0.1"
Read ontoindex-navigation first.
OntoIndex CLI Commands
Run the installed ontoindex command from the target repository. Query OntoIndex first; repo queries schedule managed background refresh when stale. Only the coordinating session runs ontoindex analyze manually when immediate refresh is required and no refresh job is active; sub-agents never analyze. Never launch analyze through npx; npx can fetch a different version.
analyze indexes the repository and updates the OntoIndex block in AGENTS.md and CLAUDE.md. Use --skip-agents-md to leave those files untouched. Uncommitted edits use the automatic overlay; label stale/refreshing results and verify edited or new code from source. Embeddings are optional and off by default.
| Command | Purpose | |
|---|---|---|
ontoindex analyze [path] | Build or refresh the index; --force reindexes, --embeddings enables embeddings. | |
ontoindex status [--repo <repo>] | Show index status for the current or selected repository. | |
ontoindex list | List registered indexed repositories. | |
ontoindex mcp-doctor [--repo <repo>] [--project-cwd <path>] [--json] | Check MCP repository targeting and print repair guidance. | |
ontoindex clean | Show confirmation before deleting the current repository index. | |
ontoindex clean --generations [--keep <n>] | Preview obsolete generation cleanup; --keep retains 0–10 non-active generations (default 2). Add --force to delete candidates. | |
ontoindex clean --all --force | Delete indexes for every registered repository. This is destructive; ask the user before running it. | |
ontoindex wiki [path] | Generate repository documentation with an external LLM. Run only on explicit user request. |
wiki can publish a public GitHub Gist with --gist. Prefer ONTOINDEX_API_KEY or OPENAI_API_KEY from the environment; avoid putting secrets on the command line. The CLI also accepts --api-key <key> and saves it in ~/.ontoindex/config.json.