Doctor now compares generated agent/skill counts against the source directories and the rule-skills manifest, parses installed settings.json as JSON, sanity-checks installed config.toml for balanced quotes and brackets, scans generated output for leftover template placeholders, and reports missing or locally modified files from each destination's managed manifest. All checks stay local and file-based; no network calls. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>