fix: harden gbrain upgrade and repair flows

[prashant-em]

Summary

• fix read-only skillpack commands so they work outside the repo root using an install-path fallback
• update post-upgrade advisory text to recommend gbrain skillpack scaffold instead of the removed install flow
• make gbrain frontmatter validate --fix actually repair missing frontmatter and common YAML parse failures
• stop false-positive NESTED_QUOTES warnings for valid quoted YAML arrays
• point doctor graph-coverage remediation at the DB-backed extractor command it actually means

Verification

• bun test test/brain-writer.test.ts test/frontmatter-cli.test.ts test/markdown-validation.test.ts test/post-install-advisory.test.ts test/skillpack-install.test.ts test/doctor.test.ts
• gbrain frontmatter validate /Users/prashantagarwal/gbrain-sources/hq-curated --fix --json
• gbrain frontmatter validate /Users/prashantagarwal/gbrain-sources/hq-curated --json
• gbrain doctor --json || true
• gbrain extract all --source db

Notes

• Direct push to upstream garrytan/gbrain was blocked with HTTP 403, so this ships via fork + PR.