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>

CHANGELOG.md

@@ -26,6 +26,35 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Installation process detects and migrates existing commands automatically
 - Tab completion support for `/sc:` prefix to discover all SuperClaude commands
 
+## [4.0.0-beta.1] - 2025-02-05
+
+### Added
+- **Agent System**: 13 specialized domain experts replacing personas
+- **Behavioral Modes**: 4 intelligent modes for different workflows (Brainstorming, Introspection, Task Management, Token Efficiency)
+- **Session Lifecycle**: /sc:load and /sc:save for cross-session persistence with Serena MCP
+- **New Commands**: /sc:brainstorm, /sc:reflect, /sc:save, /sc:select-tool (21 total commands)
+- **Serena MCP**: Semantic code analysis and memory management
+- **Morphllm MCP**: Intelligent file editing with Fast Apply capability
+- **Hooks System**: Python-based framework integration (completely redesigned and implemented)
+- **SuperClaude-Lite**: Minimal implementation with YAML configuration
+- **Templates**: Comprehensive templates for creating new components
+- **Python-Ultimate-Expert Agent**: Master Python architect for production-ready code
+
+### Changed
+- Commands expanded from 16 to 21 specialized commands
+- Personas replaced with 13 specialized Agents
+- Enhanced MCP integration (6 servers total)
+- Improved token efficiency (30-50% reduction with Token Efficiency Mode)
+- Session management now uses Serena integration for persistence
+- Framework structure reorganized for better modularity
+
+### Improved
+- Task management with multi-layer orchestration (TodoWrite, /task, /spawn, /loop)
+- Quality gates with 8-step validation cycle
+- Performance monitoring and optimization
+- Cross-session context preservation
+- Intelligent routing with ORCHESTRATOR.md enhancements
+
 ## [3.0.0] - 2025-07-14
 
 ### Added