refactor: Clean up docs/ directory structure

📚 Documentation Organization:
- Move 9 historical files to docs/archive/ (session summaries, implementation status)
- Keep only 5 current reference docs in docs/ (safety, build, LLM guide)
- Update docs/README.md with clean structure and current status

✨ Clean docs/ Structure:
├── README.md (updated directory index)
├── SACRED_TRUST_SAFETY.md (core safety framework)
├── UV_BUILD_GUIDE.md (build instructions)
├── PACKAGE_READY.md (package info)
├── LLM_TOOL_GUIDE.md (AI assistant reference)
└── archive/ (15 historical implementation docs)

🎯 Result: Professional documentation structure with clear separation
between current reference docs and historical development records.

Ready for Phase 3 with clean, maintainable project organization!

docs/README.md

@@ -1,23 +1,33 @@
-# Documentation
+# 📚 Enhanced MCP Tools Documentation
 
-This directory contains various documentation and analysis files for the Enhanced MCP Tools project.
+This directory contains reference documentation for the Enhanced MCP Tools project.
 
-## Contents
+## 📋 Current Documentation
 
-### Project Status & Completion
-- **PROJECT_COMPLETION_STATUS.md** - Main project completion summary and results
-- **SESSION_COMPLETION_SUMMARY.md** - Session-specific completion notes
+### **🛡️ Safety & Security**
+- **[SACRED_TRUST_SAFETY.md](SACRED_TRUST_SAFETY.md)** - Core safety framework for AI assistants using these tools
 
-### Feature Documentation
-- **ARCHIVE_OPERATIONS_SUMMARY.md** - Archive/compression functionality documentation
-- **GIT_DETECTION_SUMMARY.md** - Git integration features and implementation
-- **TRE_INTEGRATION_SUMMARY.md** - Tree/directory structure functionality
+### **🔧 Development & Build**
+- **[UV_BUILD_GUIDE.md](UV_BUILD_GUIDE.md)** - Build instructions using uv package manager
+- **[PACKAGE_READY.md](PACKAGE_READY.md)** - Package configuration and readiness information
 
-### Analysis & Planning
-- **ESSENTIAL_FILES_ANALYSIS.md** - Analysis of critical project files
-- **PRIORITY_TODO.md** - Priority items and future development plans
-- **LLM_TOOL_GUIDE.md** - Guide for LLM integration and usage
+### **🤖 AI Assistant Reference**
+- **[LLM_TOOL_GUIDE.md](LLM_TOOL_GUIDE.md)** - Guide for AI assistants on tool safety categories and usage
 
-## Organization
+## 📦 Historical Documentation
 
-These files were moved from the project root to improve organization and maintainability. Each file contains detailed information about specific aspects of the project implementation and status.
+The **[archive/](archive/)** directory contains historical implementation records, session summaries, and development status reports from the project's evolution. These files document the development journey but are not needed for current usage.
+
+## 🎯 Current Project Status
+
+- **Phase 1**: ✅ Complete (5/5 tools) - Essential git workflow and core functionality
+- **Phase 2**: ✅ Nearly Complete (4/5 tools) - Code quality and analysis pipeline  
+- **Phase 3**: 🎯 Ready - Enhanced UX & environment tools (developer superpowers)
+
+**Total Progress**: 9/19 tools implemented (47% complete)
+
+## 📖 Main Documentation
+
+For the primary project documentation, see the main [README.md](../README.md) in the project root.
+
+For the current development roadmap and Phase 3 plans, see [TODO.md](../TODO.md).