doctor

# Doctor Diagnose the health of your OneBrain vault and plugin configuration. Inspired by `brew doctor` and `npm doctor`. Usage: - `/doctor` — full check (vault + config + memory) - `/doctor --vault` — vault content checks only (skips CLI doctor) - `/doctor --config` — plugin config + CLI doctor only (skips vault content) - `/doctor --fix` — auto-fix safe issues (CLI fix recipes + skill fixes) **Flag detection:** Determine active flags from the user's message. `--vault` = user mentions vault-only or content health; `--config` = user mentions config or plugin check; `--fix` = user explicitly asks to fix or auto-fix. Default (no flags) = run all checks. **Two-source architecture** (post-v3.0.0 GA): - **CLI doctor** (`onebrain doctor --json`) handles the built-in checks, grouped into four sections: **Config** (onebrain.yml, onebrain.yml-keys, vault-config-migration, legacy-qmd-collection), **Vault structure** (folders, plugin-files, plugin-cache), **Integration** (settings-hooks, claude-settings), **Index & state** (orphan-checkpoints, search). Rust-native, single subprocess call, structured JSON output. (`search` replaced the v3.3 `qmd-embeddings` probe; `legacy-qmd-collection` migrates a top-level `qmd_collection` → `search.collection`.) - **Skill checks** handle vault-content + state-machine checks the CLI doesn't cover: broken wikilinks, orphan notes, stale memory/ files, MEMORY.md size, inbox backlog, log folder size, scheduler health, pause-thread state, memory health....