Complete three-tier config migration (gt-k1lr)

- Add doctor checks for new config architecture:
  - SettingsCheck: Verify rigs have settings/ directory
  - RuntimeGitignoreCheck: Verify .runtime/ is gitignored
  - LegacyGastownCheck: Detect/remove old .gastown/ dirs
- Update .gitignore to include .runtime/
- Update architecture.md with new directory structure
- Update hq.md to clarify PGT vs GGT config locations

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

.gitignore

@@ -28,3 +28,4 @@ gt
 
 # Runtime state
 state.json
+.runtime/