refactor: Clean up and organize root directory documentation

🧹 Root Directory Cleanup:
- Remove 9 outdated .md files from root directory
- Keep only essential docs in root (README.md, TODO.md)

📚 Reorganized Documentation:
- Move important docs to docs/: SACRED_TRUST_SAFETY.md, UV_BUILD_GUIDE.md, PACKAGE_READY.md
- Archive historical files in docs/archive/: implementation status docs, fix summaries
- Remove duplicate TODO file (kept TODO.md as primary)

✨ Result: Clean root directory with logical documentation structure
📁 Structure: root (essential) → docs/ (reference) → docs/archive/ (historical)

Improves project maintainability and reduces root directory clutter.

TODO

@@ -1,252 +0,0 @@
-# Enhanced MCP Tools - TODO
-
-## ✅ COMPLETED - Project Validation & Implementation
-
-### Phase 1: Core Framework ✅ DONE
-- [x] **FastMCP Integration** - MCPMixin pattern implemented
-- [x] **Tool Organization** - 11 categories with prefixes
-- [x] **Error Handling** - Comprehensive try/catch blocks
-- [x] **Type Safety** - Full type hints and Literal types
-- [x] **Context Logging** - Proper MCP Context usage
-
-### Phase 2: Tool Implementation ✅ DONE (37/37 tools)
-
-#### Diff/Patch Operations ✅ 3/3
-- [x] `diff_generate_diff` - System diff command integration
-- [x] `diff_apply_patch` - Patch application with dry-run support
-- [x] `diff_create_patch_file` - Generate patches from edits
-
-#### Git Integration ✅ 3/3  
-- [x] `git_git_status` - Repository status with GitPython
-- [x] `git_git_diff` - Diff generation and formatting
-- [x] `git_git_commit_prepare` - Commit staging with AI suggestions
-
-#### Enhanced File Operations ✅ 7/7 - **ENHANCED WITH TRE & GIT DETECTION**
-- [x] `file_watch_files` - Real-time monitoring with watchdog
-- [x] `file_bulk_rename` - Regex-based pattern renaming
-- [x] `file_file_backup` - Timestamped backups with compression
-- [x] `file_list_directory_tree` - Comprehensive directory tree with JSON metadata, git status, filtering
-- [x] `file_tre_directory_tree` - **NEW** Lightning-fast LLM-optimized tree using Rust-based 'tre' command
-- [x] `file_tre_llm_context` - **NEW** Complete LLM context generation with tree + file contents
-- [x] `file_enhanced_list_directory` - **NEW** Enhanced directory listing with automatic git repository detection
-
-#### Advanced Search & Analysis ✅ 3/3
-- [x] `search_search_and_replace_batch` - Multi-file find/replace
-- [x] `search_analyze_codebase` - LOC, complexity, dependencies
-- [x] `search_find_duplicates` - Hash-based duplicate detection
-
-#### Development Workflow ✅ 3/3
-- [x] `dev_run_tests` - pytest/jest framework detection
-- [x] `dev_lint_code` - flake8/pylint/black integration
-- [x] `dev_format_code` - black/prettier auto-formatting
-
-#### Network & API Tools ✅ 2/2
-- [x] `net_http_request` - httpx-based HTTP client
-- [x] `net_api_mock_server` - Mock server placeholder
-
-#### Archive & Compression ✅ 4/4 - **ENHANCED**
-- [x] `archive_create_archive` - Multi-format archive creation (tar, tar.gz, tgz, tar.bz2, tar.xz, zip)
-- [x] `archive_extract_archive` - Secure multi-format extraction with path traversal protection
-- [x] `archive_list_archive` - Non-destructive content listing with detailed metadata
-- [x] `archive_compress_file` - Individual file compression (gzip, bzip2, xz, lzma)
-
-#### Process Tracing ✅ 3/3
-- [x] `trace_trace_process` - Process tracing placeholder
-- [x] `trace_analyze_syscalls` - Syscall analysis placeholder  
-- [x] `trace_process_monitor` - Real-time monitoring placeholder
-
-#### Environment Management ✅ 3/3
-- [x] `env_environment_info` - System/Python/Node/Git info
-- [x] `env_process_tree` - psutil-based process hierarchy
-- [x] `env_manage_virtual_env` - venv creation and management
-
-#### Enhanced Existing Tools ✅ 3/3
-- [x] `enhanced_execute_command_enhanced` - Advanced command execution
-- [x] `enhanced_search_code_enhanced` - Semantic search placeholder
-- [x] `enhanced_edit_block_enhanced` - Multi-file editing placeholder
-
-#### Utility Tools ✅ 3/3
-- [x] `util_generate_documentation` - Documentation generation placeholder
-- [x] `util_project_template` - Project scaffolding placeholder
-- [x] `util_dependency_check` - requirements.txt/package.json analysis
-
-### Phase 3: Documentation & Testing ✅ DONE
-- [x] **README.md** - Comprehensive documentation
-- [x] **API Documentation** - Tool descriptions and parameters
-- [x] **Usage Examples** - Configuration and deployment
-- [x] **Test Scripts** - Server validation and comparison
-- [x] **Configuration Examples** - Claude Desktop integration
-
-### Phase 4: Validation ✅ DONE
-- [x] **Import Testing** - Server imports successfully
-- [x] **Registration Testing** - All tools register correctly
-- [x] **Startup Testing** - Server starts without errors
-- [x] **Coverage Analysis** - 100% tool implementation coverage
-- [x] **Comparison Analysis** - Matches initial design exactly
-
----
-
-## 🚀 PROJECT STATUS: ✅ PRODUCTION READY - ALL FEATURES IMPLEMENTED
-
-### ✅ ALL IMPLEMENTATION GOALS ACHIEVED - June 23, 2025
-- **All 37+ tools implemented** (100% coverage)
-- **All missing methods added and fully functional**
-- **All tests passing** (11/11 tests - 0 warnings)
-- **Server starts successfully** with all tools registered
-- **Comprehensive error handling** and logging throughout
-- **Full type safety** with proper async/await patterns
-- **Production-ready code quality**
-
-### 🎯 COMPLETED TODAY - Implementation Sprint (June 23, 2025)
-
-#### ✅ NEW FILE OPERATIONS METHODS IMPLEMENTED
-- **✅ `list_directory_tree`** - Comprehensive directory tree with JSON metadata, git status, filtering
-- **✅ `tre_directory_tree`** - Lightning-fast Rust-based tree scanning for LLM optimization  
-- **✅ `tre_llm_context`** - Complete LLM context with tree + file contents
-- **✅ `enhanced_list_directory`** - Enhanced listing with automatic git repository detection
-
-#### ✅ SEARCH ANALYSIS IMPLEMENTATION COMPLETED
-- **✅ `analyze_codebase`** - Full implementation with LOC analysis, complexity metrics, dependency detection
-
-#### ✅ ALL TEST FAILURES RESOLVED
-- **✅ test_directory_tree.py** - Fixed tree structure and field expectations
-- **✅ test_git_detection.py** - Implemented proper git integration with expected field names
-- **✅ test_basic.py** - Fixed class references and method implementations
-- **✅ test_functional.py** - Removed invalid method calls, all tools working
-- **✅ test_tre_functionality.py** - tre integration working with fallbacks
-
-#### ✅ CODE QUALITY IMPROVEMENTS
-- **✅ Fixed all import statements** - Added fnmatch, subprocess where needed
-- **✅ Resolved all deprecation warnings** - Updated tar.extract() with filter parameter
-- **✅ Fixed test assertion patterns** - Changed return statements to proper assert statements
-- **✅ Path resolution fixes** - Corrected project root detection in tests
-- **✅ Field name standardization** - Aligned implementation with test expectations
-
-#### ✅ ERROR HANDLING & ROBUSTNESS  
-- **✅ Comprehensive try/catch blocks** throughout all new methods
-- **✅ Context logging integration** for all operations
-- **✅ Graceful fallbacks** (tre → tree → python implementation)
-- **✅ Type safety** with proper Optional and Literal types
-- **✅ Input validation** and sanitization
-
-### 📊 FINAL TEST RESULTS
-```
-============================= test session starts ==============================
-collected 11 items
-
-tests/test_archive_operations.py .                                       [  9%]
-tests/test_basic.py ..                                                   [ 27%]
-tests/test_directory_tree.py .                                           [ 36%]
-tests/test_functional.py .                                               [ 45%]
-tests/test_git_detection.py .                                            [ 54%]
-tests/test_modular_structure.py ...                                      [ 81%]
-tests/test_server.py .                                                   [ 90%]
-tests/test_tre_functionality.py .                                        [100%]
-
-============================== 11 passed in 0.81s ==============================
-```
-
-**Result: 11/11 TESTS PASSING - 0 WARNINGS - 0 ERRORS**
-
-### 🎉 PRODUCTION DEPLOYMENT STATUS
-
-The Enhanced MCP Tools project is now **FULLY COMPLETE** and ready for:
-
-- ✅ **Production deployment** - All systems functional
-- ✅ **Claude Desktop integration** - Server starts reliably  
-- ✅ **Development workflows** - All 50+ tools operational
-- ✅ **Community distribution** - Solid, tested foundation
-
----
-
-## 📜 HISTORICAL COMPLETION LOG
-
-### ✅ All Initial Design Goals Achieved
-- **37 tools implemented** (100% coverage)
-- **11 tool categories** organized
-- **Async/await throughout** 
-- **Comprehensive error handling**
-- **Full type safety**
-- **Production-ready code quality**
-
-### 🎯 Recent Enhancements
-- **✅ Archive Operations Enhanced** (June 2025)
-  - Added comprehensive format support: tar, tar.gz, tgz, tar.bz2, tar.xz, zip
-  - Implemented security features: path traversal protection, safe extraction
-  - Added individual file compression: gzip, bzip2, xz, lzma algorithms
-  - Full test coverage with uv integration validated
-
-- **✅ Directory Tree Listing Added** (June 2025)
-  - **NEW** `file_list_directory_tree` tool for comprehensive metadata collection
-  - JSON output with file metadata (permissions, timestamps, sizes, git status)
-  - Advanced filtering: depth control, hidden files, exclude patterns, size thresholds
-  - Git integration: shows file status when in repository
-  - Production-ready for CI/CD, analysis, and reporting use cases
-
-- **✅ tre Integration - LLM-Optimized Performance** (June 2025)
-  - **NEW** `file_tre_directory_tree` - Lightning-fast Rust-based tree scanning
-  - **NEW** `file_tre_llm_context` - Complete LLM context with tree + file contents
-  - 🚀 **Performance**: Rust-based tre command for ultra-fast directory scanning
-  - 🤖 **LLM-Optimized**: Clean JSON output specifically designed for LLM consumption
-  - 🔧 **Advanced Options**: Editor aliases, portable paths, regex exclusions
-  - 📊 **Rich Metadata**: Execution time, statistics, command tracking
-  - 🎯 **Use Cases**: Code review, documentation analysis, CI/CD integration
-
-- **✅ Git Repository Detection - _PROMPTS Item #1 Complete** (June 2025)
-  - **NEW** `file_enhanced_list_directory` - Smart directory listing with git repository flags
-  - 🔄 **Auto-Detection**: Automatically flags files/directories in git repositories
-  - 📊 **Rich Git Info**: Repository root, current branch, git type detection
-  - 🎯 **Universal Integration**: All file listing tools now include git repository awareness
-  - 🔧 **Edge Case Handling**: Robust detection for worktrees, submodules, bare repos
-  - 📋 **Summary Statistics**: Counts of git-tracked vs non-git items
-
-### 🎯 Future Enhancement Opportunities
-
-#### Implementation Improvements (Optional)
-- [ ] **Process Tracing** - Add platform-specific strace/dtrace integration
-- [ ] **Mock API Server** - Implement full web framework integration  
-- [ ] **Documentation Generation** - Add sphinx/mkdocs integration
-- [ ] **Project Templates** - Add cookiecutter template support
-- [ ] **Semantic Search** - Add vector embeddings for code search
-- [ ] **Advanced Editing** - Add conflict resolution and rollback support
-
-#### Additional Tool Categories (Optional)
-- [ ] **Database Tools** - SQL query execution, schema analysis
-- [ ] **Cloud Integration** - AWS/GCP/Azure resource management
-- [ ] **Security Tools** - Vulnerability scanning, secret detection
-- [ ] **Performance Tools** - Profiling, benchmarking, monitoring
-- [ ] **AI/ML Tools** - Model training, inference, data processing
-
-#### Platform Enhancements (Optional)
-- [ ] **Web UI** - Browser-based tool interface
-- [ ] **CLI Interface** - Standalone command-line tool
-- [ ] **Plugin System** - Dynamic tool loading
-- [ ] **Configuration Management** - Advanced settings and profiles
-- [ ] **Metrics & Analytics** - Usage tracking and optimization
-
----
-
-## 📋 Maintenance Tasks
-
-### Regular Updates
-- [ ] Keep FastMCP dependency updated
-- [ ] Update Python type hints as language evolves
-- [ ] Refresh documentation examples
-- [ ] Add new file format support as needed
-
-### Community Contributions
-- [ ] Accept PRs for new tool implementations
-- [ ] Review and integrate community feedback
-- [ ] Maintain backward compatibility
-- [ ] Provide migration guides for breaking changes
-
-######
-Prompt used to start working on this project:
-
-resume using desktop commander mcp to work on /home/rpm/claude/enhanced-mcp-tools
- * use uv to run python commands*
-#####
-
----
-
-**Note**: The core project is **COMPLETE** and ready for production use. All items above this point represent optional enhancements that could be added based on user needs and community feedback.