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

templates/manifest.json

@@ -0,0 +1,24 @@
+{
+  "name": "pr-agent-auto-review",
+  "url": "https://github.com/asepharyana",
+  "hook_attributes": {
+    "url": "https://pr-agent.asepharyana.my.id/api/v1/github_webhooks",
+    "active": true
+  },
+  "redirect_url": "https://pr-agent.asepharyana.my.id/setup/callback",
+  "callback_urls": [
+    "https://pr-agent.asepharyana.my.id/setup/callback"
+  ],
+  "public": false,
+  "default_events": [
+    "pull_request",
+    "issue_comment"
+  ],
+  "default_permissions": {
+    "pull_requests": "write",
+    "issues": "write",
+    "contents": "read",
+    "metadata": "read",
+    "checks": "write"
+  }
+}