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/setup_app.py

@@ -0,0 +1,95 @@
+#!/usr/bin/env python3
+"""
+PR-Agent GitHub App Setup Helper
+Creates the GitHub App manifest and prepares the server configuration.
+"""
+import json
+import base64
+import os
+import secrets
+
+# ============================================================
+# CONFIGURATION
+# ============================================================
+APP_NAME = "pr-agent-auto"
+APP_SLUG = "pr-agent-auto"
+DESCRIPTION = "Automated PR review and merge bot powered by AI"
+HOME_URL = "https://github.com/asepharyana"
+PUBLIC_IP = "45.127.35.244"
+PORT = 4002
+WEBHOOK_URL = "https://pr-agent.asepharyana.my.id/api/v1/github_webhooks"
+REDIRECT_URL = "https://pr-agent.asepharyana.my.id/app-setup-complete"
+CALLBACK_URLS = ["https://pr-agent.asepharyana.my.id/callback"]
+
+# Generate webhook secret
+WEBHOOK_SECRET = secrets.token_hex(20)
+
+# ============================================================
+# CREATE MANIFEST
+# ============================================================
+manifest = {
+    "name": APP_NAME,
+    "slug": APP_SLUG,
+    "description": DESCRIPTION,
+    "url": HOME_URL,
+    "hook_attributes": {
+        "url": WEBHOOK_URL,
+        "active": True
+    },
+    "redirect_url": REDIRECT_URL,
+    "callback_urls": CALLBACK_URLS,
+    "public": False,
+    "default_events": [
+        "pull_request",
+        "issue_comment",
+        "push"
+    ],
+    "default_permissions": {
+        "pull_requests": "write",
+        "issues": "write",
+        "metadata": "read",
+        "contents": "read",
+        "checks": "write",
+        "emails": "read"
+    }
+}
+
+# Save manifest
+os.makedirs("/opt/pr-agent-server", exist_ok=True)
+manifest_path = "/opt/pr-agent-server/manifest.json"
+
+with open(manifest_path, "w") as f:
+    json.dump(manifest, f, indent=2)
+
+# Create the URL
+manifest_b64 = base64.b64encode(json.dumps(manifest).encode()).decode()
+manifest_url = f"https://github.com/settings/apps/new?manifest={manifest_b64}"
+
+print("=" * 60)
+print("PR-Agent GITHUB APP SETUP")
+print("=" * 60)
+print(f"\n📋 App Name: {APP_NAME}")
+print(f"🌐 Webhook URL: {WEBHOOK_URL}")
+print(f"🔑 Webhook Secret: {WEBHOOK_SECRET}")
+print(f"\n{'=' * 60}")
+print("STEP 1: Click this URL to create the GitHub App:")
+print(f"{'=' * 60}")
+print(f"\n{manifest_url}\n")
+print(f"{'=' * 60}")
+print("STEP 2: After clicking 'Create GitHub App', you'll be redirected.")
+print("   Save the App ID, Private Key, and Webhook Secret shown.")
+print(f"{'=' * 60}")
+
+# Save vars for later use
+env_file = "/opt/pr-agent-server/.env"
+with open(env_file, "w") as f:
+    f.write(f"WEBHOOK_SECRET={WEBHOOK_SECRET}\n")
+    f.write(f"PORT={PORT}\n")
+    f.write("# After GitHub App creation, add:\n")
+    f.write("# APP_ID=<your-app-id>\n")
+    f.write("# PRIVATE_KEY_PATH=/opt/pr-agent-server/private-key.pem\n")
+    f.write(f"# GITHUB_APP_NAME={APP_NAME}\n")
+
+print(f"\n📁 Config saved to: {manifest_path}")
+print(f"📁 Env file: {env_file}")
+print(f"\nWebhook Secret (save this!): {WEBHOOK_SECRET}")