docs: Comprehensive documentation update for SuperClaude V4 Beta

Updated all root documentation to reflect V4 Beta capabilities:

Root Documentation:
- VERSION: Updated to 4.0.0-beta.1
- README.md: Complete rewrite with V4 features (21 commands, 13 agents, 6 MCP servers)
- ARCHITECTURE_OVERVIEW.md: Updated for V4 Beta with correct counts and new features
- CHANGELOG.md: Added comprehensive V4.0.0-beta.1 release section
- ROADMAP.md: Added V4 Beta current status and updated future vision
- CONTRIBUTING.md: Updated architecture, testing, and contribution guidelines
- SECURITY.md: Added V4 security features and version support table
- MANIFEST.in: Updated to include new V4 directories
- pyproject.toml: Updated URLs and description for V4 Beta

User Documentation:
- commands-guide.md: Updated to 21 commands with new V4 commands
- superclaude-user-guide.md: Comprehensive V4 Beta features documentation
- flags-guide.md: Updated with new V4 flags and agent system
- installation-guide.md: V4 Beta installation including hooks system
- agents-guide.md: NEW - Complete guide for 13 specialized agents
- personas-guide.md: Renamed to personas-guide-v3-legacy.md

Key V4 Beta Features Documented:
- 21 specialized commands (added: brainstorm, reflect, save, select-tool)
- 13 domain expert agents replacing persona system
- 6 MCP servers (added Morphllm and Serena)
- 4 Behavioral Modes (Brainstorming, Introspection, Task Management, Token Efficiency)
- Session Lifecycle with cross-session persistence
- Redesigned Hooks System with Python integration
- SuperClaude-Lite minimal implementation
- Comprehensive Templates system

All documentation maintains friendly, accessible tone while accurately reflecting V4 Beta's advanced capabilities.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

SECURITY.md

@@ -49,13 +49,23 @@ When reporting a vulnerability, please provide:
 - Configuration issues with security implications
 - Dependency vulnerabilities with low exploitability
 
+## 🔐 Supported Versions
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 4.0.0-beta.x | ✅ Active Development |
+| 3.0.x   | ⚠️ Security fixes only |
+| < 3.0   | ❌ End of life |
+
 ## 🛡️ Security Features
 
-### Hook Execution Security
-- **Timeout protection**: All hooks have configurable timeouts
+### Hook Execution Security (V4 Enhanced)
+- **Timeout protection**: All hooks have configurable timeouts (default 30s)
 - **Input validation**: JSON schema validation for all hook inputs
 - **Sandboxed execution**: Hooks run with limited system permissions
 - **Error containment**: Hook failures don't affect framework stability
+- **Performance monitoring**: Real-time hook execution tracking
+- **Session lifecycle integration**: Secure checkpoint and recovery
 
 ### File System Protection
 - **Path validation**: Prevents directory traversal attacks
@@ -63,11 +73,13 @@ When reporting a vulnerability, please provide:
 - **Secure defaults**: Conservative file access patterns
 - **Backup mechanisms**: Safe fallback when operations fail
 
-### MCP Server Security
+### MCP Server Security (6 Servers in V4)
 - **Server validation**: Verify MCP server authenticity and integrity
 - **Communication encryption**: Secure channels for all MCP communication
 - **Timeout handling**: Prevent resource exhaustion from unresponsive servers
 - **Fallback mechanisms**: Graceful degradation when servers are compromised
+- **Serena MCP**: Secure memory management with access controls
+- **Morphllm MCP**: Validated file editing with permission checks
 
 ### Configuration Security
 - **Input sanitization**: All configuration inputs are validated and sanitized
@@ -194,7 +206,7 @@ For general security questions (not vulnerabilities):
 
 ---
 
-**Last Updated**: July 2025  
-**Next Review**: October 2025
+**Last Updated**: February 2025 (V4 Beta)  
+**Next Review**: May 2025
 
 Thank you for helping keep SuperClaude Framework secure! 🙏