AutoRAG doctor

Goal: every configured datasource is indexed and actually returns hits. A green status is not enough, the run is done only when a real query returns a real hit per datasource, or the datasource is reported as genuinely empty or not configured.

Always finish with the status table in Report.

Safety

• Diagnosis and repair never delete, move, or edit source documents; a doctor run changes only AutoRAG-owned state.
• Never delete a datasource's native store (~/Library/Application Support/katok, ~/.discrawl, ~/.mailcrawl, Telegram/WhatsApp/Notion archives). AutoRAG only reads them; rebuilding them is the owning CLI's job.
• Only AutoRAG-owned state under AUTORAG_HOME and the workspace .autorag directory may be reset.
• Never print token or password values. Report credential names only.
• Kill a process only after confirming it is an AutoRAG-owned orphan.

1. Triage the core

autorag status --json
autorag health --json
autorag setup --format json

• status reports state, stale, diagnostics, and per-component state for minsync, jikji, and datasources. stale: true or any stale-index diagnostic means the corpus changed since the last successful refresh.
• health resolves the single search model and does one live completion probe. --skip-probes only proves config shape, never live access; do not claim a healthy model from it.
• setup --format json reports embedding.backend (remote, daemon, or in-process) and the resolved provider/model/dimension when a backend is alive, or embedding.reason and a remediation when none is. It only probes; it never starts a daemon. Semantic search needs the daemon (or a remote endpoint) to be running: a backend that is absent is a real embedding-unavailable state, not normal.