refactor: restructure into proper project layout + improve docs

Project layout:
- src/: application modules (run_server, auto_merge_bot, health-check, sync-key, trivial_merge, callback_server, start_server)
- scripts/: setup/deployment helpers (setup_all, setup_app, generate_manifest)
- templates/: manifest.json (GitHub App manifest template)
- docs/  + CONTRIBUTING.md: documentation

Improvements:
- flake.nix: added pr-agent-auto-merge wrapper binary, updated installPhase paths
- deploy.yml: syntax check covers all modules including health-check.py and sync-key.py
- README.md: comprehensive with architecture, layout, dev, ops, deployment
- CONTRIBUTING.md: standards and testing checklist
- .gitignore: added *.log, *.pid, .env.*
- Cleanup: removed duplicate manifest_current.json / manifest_final.json
- Fix: health-check.py docstring updated to claude-opus-5

Verification:
- ✅ python3 -m py_compile: all 11 modules pass
- ✅ nix flake check: passes

.gitignore

@@ -5,13 +5,20 @@ webhook_secret.txt
 whsec*.txt
 .secrets.toml
 .env
+.env.*
 
 # Python
 __pycache__/
 *.pyc
 result
+
+# Packaging
 *.egg-info/
 .eggs/
 dist/
 build/
 .venv/
+
+# Runtime data
+*.log
+*.pid