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

scripts/generate_manifest_domain.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+"""Generate GitHub App manifest with domain URL"""
+import json
+import base64
+import secrets
+
+webhook_secret = secrets.token_hex(20)
+print(f"Webhook Secret: {webhook_secret}")
+
+manifest = {
+    "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"
+    }
+}
+
+manifest_json = json.dumps(manifest)
+manifest_b64 = base64.urlsafe_b64encode(manifest_json.encode()).decode()
+
+print(f"\n{'='*60}")
+print("BUAT APP BARU - Klik link ini di browser GitHub:")
+print(f"{'='*60}")
+print(f"https://github.com/settings/apps/new?manifest={manifest_b64}")
+print(f"{'='*60}")
+
+# Save
+with open("/opt/pr-agent-server/manifest_domain.json", "w") as f:
+    json.dump(manifest, f, indent=2)
+with open("/opt/pr-agent-server/webhook_secret.txt", "w") as f:
+    f.write(webhook_secret)
+
+print(f"\nWebhook secret: {webhook_secret}")
+print(f"Webhook URL: https://pr-agent.asepharyana.my.id/api/v1/github_webhooks")