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- Restructured all documentation under unified Docs/ directory
- Removed outdated phase summaries and consolidated content
- Added comprehensive Reference section with 11 new guides:
* Advanced patterns and workflows
* Basic examples and common issues
* Integration patterns and MCP server guides
* Optimization and diagnostic references
- Enhanced User-Guide with updated agent and mode documentation
- Updated MCP configurations for morphllm and serena
- Added TODO.md for project tracking
- Maintained existing content quality while improving organization
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Co-Authored-By: Claude <noreply@anthropic.com>