From de512018cf99ad5749574db6f4ed01589e1faa14 Mon Sep 17 00:00:00 2001 From: Ryan Malloy Date: Mon, 23 Jun 2025 13:50:17 -0600 Subject: [PATCH] refactor: Clean up and organize root directory documentation MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit ๐Ÿงน Root Directory Cleanup: - Remove 9 outdated .md files from root directory - Keep only essential docs in root (README.md, TODO.md) ๐Ÿ“š Reorganized Documentation: - Move important docs to docs/: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) โœจ Result: Clean root directory with logical documentation structure ๐Ÿ“ Structure: root (essential) โ†’ docs/ (reference) โ†’ docs/archive/ (historical) Improves project maintainability and reduces root directory clutter. --- TODO | 252 ------------------ PACKAGE_READY.md => docs/PACKAGE_READY.md | 0 .../SACRED_TRUST_SAFETY.md | 0 UV_BUILD_GUIDE.md => docs/UV_BUILD_GUIDE.md | 0 .../archive/CONTEXT_API_FIX.md | 0 .../archive/CRITICAL_ERROR_HANDLING.md | 0 .../archive/EMERGENCY_LOGGING_COMPLETE.md | 0 .../archive/EMERGENCY_LOGGING_GUIDE.md | 0 .../archive/IMPLEMENTATION_COMPLETE.md | 0 .../archive/IMPORT_FIXES_SUMMARY.md | 0 10 files changed, 252 deletions(-) delete mode 100644 TODO rename PACKAGE_READY.md => docs/PACKAGE_READY.md (100%) rename SACRED_TRUST_SAFETY.md => docs/SACRED_TRUST_SAFETY.md (100%) rename UV_BUILD_GUIDE.md => docs/UV_BUILD_GUIDE.md (100%) rename CONTEXT_API_FIX.md => docs/archive/CONTEXT_API_FIX.md (100%) rename CRITICAL_ERROR_HANDLING.md => docs/archive/CRITICAL_ERROR_HANDLING.md (100%) rename EMERGENCY_LOGGING_COMPLETE.md => docs/archive/EMERGENCY_LOGGING_COMPLETE.md (100%) rename EMERGENCY_LOGGING_GUIDE.md => docs/archive/EMERGENCY_LOGGING_GUIDE.md (100%) rename IMPLEMENTATION_COMPLETE.md => docs/archive/IMPLEMENTATION_COMPLETE.md (100%) rename IMPORT_FIXES_SUMMARY.md => docs/archive/IMPORT_FIXES_SUMMARY.md (100%) diff --git a/TODO b/TODO deleted file mode 100644 index fd8c103..0000000 --- a/TODO +++ /dev/null @@ -1,252 +0,0 @@ -# Enhanced MCP Tools - TODO - -## โœ… COMPLETED - Project Validation & Implementation - -### Phase 1: Core Framework โœ… 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 โœ… DONE (37/37 tools) - -#### Diff/Patch Operations โœ… 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 โœ… 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 โœ… 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 โœ… 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 โœ… 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 โœ… 2/2 -- [x] `net_http_request` - httpx-based HTTP client -- [x] `net_api_mock_server` - Mock server placeholder - -#### Archive & Compression โœ… 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 โœ… 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 โœ… 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 โœ… 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 โœ… 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 โœ… 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 โœ… 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 - ---- - -## ๐Ÿš€ PROJECT STATUS: โœ… PRODUCTION READY - ALL FEATURES IMPLEMENTED - -### โœ… 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** - -### ๐ŸŽฏ COMPLETED TODAY - Implementation Sprint (June 23, 2025) - -#### โœ… NEW FILE OPERATIONS METHODS IMPLEMENTED -- **โœ… `list_directory_tree`** - Comprehensive directory tree with JSON metadata, git status, filtering -- **โœ… `tre_directory_tree`** - Lightning-fast Rust-based tree scanning for LLM optimization -- **โœ… `tre_llm_context`** - Complete LLM context with tree + file contents -- **โœ… `enhanced_list_directory`** - Enhanced listing with automatic git repository detection - -#### โœ… SEARCH ANALYSIS IMPLEMENTATION COMPLETED -- **โœ… `analyze_codebase`** - Full implementation with LOC analysis, complexity metrics, dependency detection - -#### โœ… ALL TEST FAILURES RESOLVED -- **โœ… test_directory_tree.py** - Fixed tree structure and field expectations -- **โœ… test_git_detection.py** - Implemented proper git integration with expected field names -- **โœ… test_basic.py** - Fixed class references and method implementations -- **โœ… test_functional.py** - Removed invalid method calls, all tools working -- **โœ… test_tre_functionality.py** - tre integration working with fallbacks - -#### โœ… CODE QUALITY IMPROVEMENTS -- **โœ… Fixed all import statements** - Added fnmatch, subprocess where needed -- **โœ… Resolved all deprecation warnings** - Updated tar.extract() with filter parameter -- **โœ… Fixed test assertion patterns** - Changed return statements to proper assert statements -- **โœ… Path resolution fixes** - Corrected project root detection in tests -- **โœ… Field name standardization** - Aligned implementation with test expectations - -#### โœ… ERROR HANDLING & ROBUSTNESS -- **โœ… Comprehensive try/catch blocks** throughout all new methods -- **โœ… Context logging integration** for all operations -- **โœ… Graceful fallbacks** (tre โ†’ tree โ†’ python implementation) -- **โœ… Type safety** with proper Optional and Literal types -- **โœ… Input validation** and sanitization - -### ๐Ÿ“Š 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** - -### ๐ŸŽ‰ PRODUCTION DEPLOYMENT STATUS - -The Enhanced MCP Tools project is now **FULLY COMPLETE** and ready for: - -- โœ… **Production deployment** - All systems functional -- โœ… **Claude Desktop integration** - Server starts reliably -- โœ… **Development workflows** - All 50+ tools operational -- โœ… **Community distribution** - Solid, tested foundation - ---- - -## ๐Ÿ“œ HISTORICAL COMPLETION LOG - -### โœ… 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** - -### ๐ŸŽฏ Recent Enhancements -- **โœ… 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 - -- **โœ… 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 - -- **โœ… 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 - - ๐Ÿš€ **Performance**: Rust-based tre command for ultra-fast directory scanning - - ๐Ÿค– **LLM-Optimized**: Clean JSON output specifically designed for LLM consumption - - ๐Ÿ”ง **Advanced Options**: Editor aliases, portable paths, regex exclusions - - ๐Ÿ“Š **Rich Metadata**: Execution time, statistics, command tracking - - ๐ŸŽฏ **Use Cases**: Code review, documentation analysis, CI/CD integration - -- **โœ… Git Repository Detection - _PROMPTS Item #1 Complete** (June 2025) - - **NEW** `file_enhanced_list_directory` - Smart directory listing with git repository flags - - ๐Ÿ”„ **Auto-Detection**: Automatically flags files/directories in git repositories - - ๐Ÿ“Š **Rich Git Info**: Repository root, current branch, git type detection - - ๐ŸŽฏ **Universal Integration**: All file listing tools now include git repository awareness - - ๐Ÿ”ง **Edge Case Handling**: Robust detection for worktrees, submodules, bare repos - - ๐Ÿ“‹ **Summary Statistics**: Counts of git-tracked vs non-git items - -### ๐ŸŽฏ 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 - ---- - -## ๐Ÿ“‹ 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. diff --git a/PACKAGE_READY.md b/docs/PACKAGE_READY.md similarity index 100% rename from PACKAGE_READY.md rename to docs/PACKAGE_READY.md diff --git a/SACRED_TRUST_SAFETY.md b/docs/SACRED_TRUST_SAFETY.md similarity index 100% rename from SACRED_TRUST_SAFETY.md rename to docs/SACRED_TRUST_SAFETY.md diff --git a/UV_BUILD_GUIDE.md b/docs/UV_BUILD_GUIDE.md similarity index 100% rename from UV_BUILD_GUIDE.md rename to docs/UV_BUILD_GUIDE.md diff --git a/CONTEXT_API_FIX.md b/docs/archive/CONTEXT_API_FIX.md similarity index 100% rename from CONTEXT_API_FIX.md rename to docs/archive/CONTEXT_API_FIX.md diff --git a/CRITICAL_ERROR_HANDLING.md b/docs/archive/CRITICAL_ERROR_HANDLING.md similarity index 100% rename from CRITICAL_ERROR_HANDLING.md rename to docs/archive/CRITICAL_ERROR_HANDLING.md diff --git a/EMERGENCY_LOGGING_COMPLETE.md b/docs/archive/EMERGENCY_LOGGING_COMPLETE.md similarity index 100% rename from EMERGENCY_LOGGING_COMPLETE.md rename to docs/archive/EMERGENCY_LOGGING_COMPLETE.md diff --git a/EMERGENCY_LOGGING_GUIDE.md b/docs/archive/EMERGENCY_LOGGING_GUIDE.md similarity index 100% rename from EMERGENCY_LOGGING_GUIDE.md rename to docs/archive/EMERGENCY_LOGGING_GUIDE.md diff --git a/IMPLEMENTATION_COMPLETE.md b/docs/archive/IMPLEMENTATION_COMPLETE.md similarity index 100% rename from IMPLEMENTATION_COMPLETE.md rename to docs/archive/IMPLEMENTATION_COMPLETE.md diff --git a/IMPORT_FIXES_SUMMARY.md b/docs/archive/IMPORT_FIXES_SUMMARY.md similarity index 100% rename from IMPORT_FIXES_SUMMARY.md rename to docs/archive/IMPORT_FIXES_SUMMARY.md