v0.1.16: Security overhaul and systematic deployment preparation

Breaking changes for clean alpha releases:
- JWT authentication with user-provided secrets (no more development defaults)
- Registration token system for secure agent enrollment
- Rate limiting with user-adjustable settings
- Enhanced agent configuration with proxy support
- Interactive server setup wizard (--setup flag)
- Heartbeat architecture separation for better UX
- Package status synchronization fixes
- Accurate timestamp tracking for RMM features

Setup process for new installations:
1. docker-compose up -d postgres
2. ./redflag-server --setup
3. ./redflag-server --migrate
4. ./redflag-server
5. Generate tokens via admin UI
6. Deploy agents with registration tokens

.gitignore

@@ -404,4 +404,19 @@ secrets/
 # =============================================================================
 # AI / LLM Development Files
 # =============================================================================
-.claude/
+.claude/
+
+# =============================================================================
+# Development and deployment environments
+# =============================================================================
+website/
+deployment/
+
+# =============================================================================
+# Generated development documentation
+# =============================================================================
+docs/
+*.md
+!README.md
+!LICENSE
+!.env.example