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

.github/workflows/deploy.yml

@@ -26,7 +26,7 @@ jobs:
 
       - name: Python syntax check
         run: |
-          python3 -m py_compile run_server.py auto_merge_bot.py callback_server.py setup_app.py setup_all.py generate_manifest.py generate_manifest_domain.py start_server.py
+          python3 -m py_compile src/run_server.py src/auto_merge_bot.py src/callback_server.py scripts/setup_app.py scripts/setup_all.py scripts/generate_manifest.py scripts/generate_manifest_domain.py src/start_server.py src/sync-key.py src/health-check.py src/trivial_merge.py
 
   build-and-deploy:
     needs: syntax-check