Code-Index-MCP

# Comprehensive Markdown Documentation Index Generated: 2025-01-30 ## Overview This index provides a complete catalog of all markdown documentation in the Code-Index-MCP project, organized by purpose, context (AI Agent vs Human), and content type. ### Summary Statistics - **Total Markdown Files**: 70 (including new index files) - **AI Agent Context Files**: 20 (CLAUDE.md, AGENTS.md, and index files) - **Human Documentation Files**: 50 - **Total Documentation Size**: ~750KB (increased due to enhanced plugin guides) - **Largest File**: `/ai_docs/qdrant.md` (50.9KB) - **Smallest File**: Multiple CLAUDE.md stub files (302 bytes each) - **Enhanced Plugin Guides**: 5 files (~55KB total) ## File Classification ### 🤖 AI AGENT CONTEXT FILES #### Primary Agent Instructions | File | Purpose | Size | Status | Key Information | |------|---------|------|--------|-----------------| | `/CLAUDE.md` | Main AI agent entry point | 302B | STUB | Points to AGENTS.md | | `/AGENTS.md` | Primary agent configuration | 3.2KB | ACTIVE | Current state (~20% implemented), capabilities, constraints | | `/markdown-table-of-contents.md` | AI agent documentation index | 6.4KB | ACTIVE | Auto-generated index with agent instructions | | `/MARKDOWN_INDEX.md` | Comprehensive doc catalog | 9.8KB | ACTIVE | Detailed inventory with cross-references | #### Architecture Agent Files | File | Purpose | Size | Status | Key Information | |------|---------|------|--------|-----------------| | `/architecture/CLAUDE.md` | Architecture context stub | 302B | STUB | Points to AGENTS.md | | `/architecture/AGENTS.md` | Architecture agent config | 1.4KB | ACTIVE | C4 model guidance, diagram operations | #### MCP Server Agent Files | File | Purpose | Size | Status | Key Information | |------|---------|------|--------|-----------------| | `/mcp_server/CLAUDE.md` | MCP server context stub | 302B | STUB | Points to AGENTS.md | | `/mcp_server/AGENTS.md` | MCP server agent config | 4.9KB | ACTIVE | Implementation status, TODOs, working features | #### Plugin Agent Files (Active) | File | Purpose | Size | Status | Key Information | |------|---------|------|--------|-----------------| | `/mcp_server/plugins/python_plugin/AGENTS.md` | Python plugin config | 2.5KB | ACTIVE | Only fully implemented plugin | | `/mcp_server/plugins/python_plugin/CLAUDE.md` | Python plugin stub | 302B | STUB | Points to AGENTS.md | #### Plugin Agent Files (Enhanced Implementation Guides) | File | Purpose | Size | Status | Key Information | |------|---------|------|--------|-----------------| | `/mcp_server/plugins/c_plugin/AGENTS.md` | C plugin implementation guide | 10.5KB | ENHANCED | Comprehensive Tree-sitter integration, preprocessor handling | | `/mcp_server/plugins/c_plugin/CLAUDE.md` | C plugin stub | 302B | STUB | Points to AGENTS.md | | `/mcp_server/plugins/cpp_plugin/AGENTS.md` | C++ plugin implementation guide | 12.3KB | ENHANCED | Templates, namespaces, modern C++ features | | `/mcp_server/plugins/cpp_plugin/CLAUDE.md` | C++ plugin stub | 302B | STUB | Points to AGENTS.md | | `/mcp_server/plugins/js_plugin/AGENTS.md` | JS plugin implementation guide | 11.8KB | ENHANCED | ES6+, modules, JSX/React support | | `/mcp_server/plugins/js_plugin/CLAUDE.md` | JS plugin stub | 302B | STUB | Points to AGENTS.md | | `/mcp_server/plugins/dart_plugin/AGENTS.md` | Dart plugin implementation guide | 11.2KB | ENHANCED | Null safety, Flutter widgets, async patterns | | `/mcp_server/plugins/dart_plugin/CLAUDE.md` | Dart plugin stub | 302B | STUB | Points to AGENTS.md | | `/mcp_server/plugins/html_css_plugin/AGENTS.md` | HTML/CSS plugin implementation guide | 10.9KB | ENHANCED | Dual parsers, preprocessors, frameworks | | `/mcp_server/plugins/html_css_plugin/CLAUDE.md` | HTML/CSS plugin stub | 302B | STUB | Points to AGENTS.md | ### 📚 HUMAN DOCUMENTATION FILES #### Project Root Documentation | File | Purpose | Size | Last Modified | Key Topics | |------|---------|------|---------------|------------| | `/README.md` | Project overview | 10.4KB | 2025-01-30 | Features, architecture, quickstart, API reference | | `/ROADMAP.md` | Development timeline | 14.3KB | 2025-01-30 | 7 phases, current status (~20%), priorities | | `/CONTRIBUTING.md` | Contribution guide | 7.1KB | 2025-01-29 | Development setup, standards, process | | `/CHANGELOG.md` | Version history | 1.7KB | 2025-01-29 | Unreleased features, planned v0.1.0 | | `/SECURITY.md` | Security policy | 1.9KB | 2025-01-29 | Vulnerability reporting, security measures | | `/TROUBLESHOOTING.md` | Common issues | 5.6KB | 2025-01-29 | Installation, startup, plugin errors | | `/DOCUMENTATION_UPDATE_SUMMARY.md` | Doc cleanup report | 4.1KB | 2025-01-30 | Cleanup actions executed, findings | | `/PHASE1_COMPLETION_SUMMARY.md` | Phase 1 status | 2.8KB | 2025-01-30 | Completed tasks, integrations, next steps | #### Architecture Documentation | File | Purpose | Size | Key Topics | |------|---------|------|------------| | `/architecture/README.md` | Architecture guide | 6.0KB | C4 model, navigation, best practices | | `/architecture/data_model.md` | Data structures | 12.2KB | SQLite schema, FTS5, relationships | | `/architecture/performance_requirements.md` | Performance specs | 3.4KB | SLAs, benchmarks, optimization | | `/architecture/security_model.md` | Security design | 5.0KB | Authentication, authorization, threats | | `/architecture/IMPLEMENTATION_GAP_ANALYSIS.md` | Gap analysis | 4.6KB | ~20% implemented, missing components | | `/architecture/ARCHITECTURE_ALIGNMENT_REPORT.md` | Alignment report | 4.1KB | Dual architecture pattern, gaps | | `/architecture/ARCHITECTURE_FIXES.md` | Architecture issues | 3.0KB | Fixes needed, consistency issues | #### API and Configuration Documentation | File | Purpose | Size | Key Topics | |------|---------|------|------------| | `/docs/api/API-REFERENCE.md` | API documentation | 6.5KB | Endpoints, request/response formats | | `/docs/configuration/ENVIRONMENT-VARIABLES.md` | Environment config | 9.1KB | All env vars, defaults, descriptions | | `/docs/DEPLOYMENT-GUIDE.md` | Deployment guide | 22.7KB | Docker, Kubernetes, production setup | | `/docs/development/TESTING-GUIDE.md` | Testing guide | 33.6KB | Unit tests, integration tests, coverage | #### AI Technology Reference Documentation | File | Purpose | Size | Technology | Use in Project | |------|---------|------|------------|----------------| | `/ai_docs/README.md` | AI docs index | 4.2KB | Overview | Technology catalog | | `/ai_docs/fastapi_overview.md` | FastAPI reference | 9.0KB | FastAPI | REST API framework | | `/ai_docs/tree_sitter_overview.md` | Tree-sitter guide | 10.2KB | Tree-sitter | Code parsing | | `/ai_docs/jedi.md` | Jedi reference | 35.2KB | Jedi | Python analysis | | `/ai_docs/pydantic_overview.md` | Pydantic guide | 15.1KB | Pydantic | Data validation | | `/ai_docs/sqlite_fts5_overview.md` | SQLite FTS5 | 29.1KB | SQLite | Full-text search | | `/ai_docs/redis.md` | Redis reference | 15.9KB | Redis | Caching (planned) | | `/ai_docs/celery_overview.md` | Celery guide | 13.7KB | Celery | Task queue (planned) | | `/ai_docs/qdrant.md` | Qdrant reference | 51.0KB | Qdrant | Vector search (planned) | | `/ai_docs/voyage_ai_overview.md` | Voyage AI guide | 5.0KB | Voyage AI | Embeddings (planned) | | `/ai_docs/watchdog.md` | Watchdog guide | 23.1KB | Watchdog | File monitoring | | `/ai_docs/grpc_overview.md` | gRPC reference | 34.0KB | gRPC | RPC (planned) | | `/ai_docs/prometheus_overview.md` | Prometheus guide | 14.8KB | Prometheus | Monitoring (planned) | | `/ai_docs/jwt_authentication_overview.md` | JWT guide | 15.4KB | JWT | Auth (planned) | | `/ai_docs/memgraph_overview.md` | Memgraph guide | 7.9KB | Memgraph | Graph DB (planned) | | `/ai_docs/plantuml_reference.md` | PlantUML guide | 9.6KB | PlantUML | Diagrams | ## Content Analysis ### Duplicate/Similar Content Identified 1. **CLAUDE.md Stubs** (9 files, 302 bytes each) - All contain identical content pointing to AGENTS.md - Recommendation: Keep as designed pattern for AI agent navigation 2. **Plugin Documentation Pattern** - Each plugin has both CLAUDE.md (stub) and AGENTS.md - Python plugin: Fully implemented with working code - Other 5 plugins: Enhanced with comprehensive implementation guides - Recommendation: Use the enhanced AGENTS.md guides when implementing each plugin 3. **Architecture Documentation** - Dual pattern: "ideal" vs "actual" architecture files - Example: `api_gateway.puml` vs `api_gateway_actual.puml` - Purpose: Track implementation progress against design ### Stale/Obsolete Documentation 1. **No obsolete files identified** - Recent documentation cleanup removed outdated files 2. **Stub plugins correctly marked** as unimplemented ### Orphaned Documentation 1. **No orphaned files found** - All documentation linked appropriately ## Cross-References ### High-Reference Files (Referenced by Multiple Documents) 1. `/README.md` - Central entry point 2. `/ROADMAP.md` - Referenced by architecture docs 3. `/architecture/` files - Referenced by AI docs and root docs 4. `/AGENTS.md` - Referenced by all CLAUDE.md files ### Key Reference Chains 1. CLAUDE.md → AGENTS.md (consistent pattern) 2. README.md → CONTRIBUTING.md, DEPLOYMENT-GUIDE.md 3. ai_docs/README.md → Individual technology files 4. Architecture files → Level 4 PlantUML diagrams ## Documentation Gaps ### Missing Documentation 1. **Plugin Development Guide** - How to create new language plugins 2. **Performance Benchmarks** - Actual measurements vs targets 3. **Migration Guide** - Moving from stubs to implementations 4. **Dispatcher Initialization Guide** - Detailed setup instructions ### Incomplete Sections 1. **CHANGELOG.md** - No released versions yet 2. **Test Documentation** - Limited automated test coverage 3. **Production Deployment** - Theoretical, not tested ### Recently Enhanced 1. **Plugin AGENTS.md files** - All 5 stub plugins now have comprehensive implementation guides 2. **Documentation indexes** - Both index files updated with current state ## Recommendations ### For AI Agents 1. **Primary References**: Start with `/AGENTS.md` and `/mcp_server/AGENTS.md` 2. **Implementation Status**: Check `IMPLEMENTATION_GAP_ANALYSIS.md` and `PHASE1_COMPLETION_SUMMARY.md` 3. **Architecture Understanding**: Use both "ideal" and "actual" architecture files ### For Human Developers 1. **Getting Started**: `/README.md` → `/CONTRIBUTING.md` → `/ROADMAP.md` 2. **Architecture**: `/architecture/README.md` → C4 model files 3. **API Development**: `/docs/api/API-REFERENCE.md` → `/ai_docs/fastapi_overview.md` 4. **Deployment**: `/docs/DEPLOYMENT-GUIDE.md` → `/docs/configuration/ENVIRONMENT-VARIABLES.md` ### Maintenance Actions 1. **Keep CLAUDE.md stubs** - They serve as navigation aids 2. **Update AGENTS.md files** when implementing features 3. **Maintain dual architecture** until implementation catches up 4. **Create plugin development guide** using Python plugin as template ## File Organization Structure ``` Code-Index-MCP/ ├── Root Documentation (Project-level) │ ├── README.md (main entry) │ ├── ROADMAP.md (timeline) │ ├── CLAUDE.md → AGENTS.md (AI context) │ └── Supporting docs (CONTRIBUTING, SECURITY, etc.) ├── architecture/ (Design & Implementation) │ ├── C4 Model files (.dsl) │ ├── level4/ (PlantUML diagrams) │ └── Analysis reports ├── ai_docs/ (Technology References) │ ├── README.md (index) │ └── Individual technology guides ├── docs/ (User Documentation) │ ├── api/ (API reference) │ ├── configuration/ (Setup guides) │ └── development/ (Dev guides) └── mcp_server/ (Implementation Docs) ├── CLAUDE.md → AGENTS.md └── plugins/ (Per-plugin docs) ``` ## Usage Patterns ### AI Agent Navigation 1. CLAUDE.md files are entry points (all point to AGENTS.md) 2. AGENTS.md files contain actual implementation details 3. Check "actual" architecture files for current state ### Human Developer Flow 1. Start with README.md for overview 2. Check ROADMAP.md for current phase 3. Use architecture/ for design understanding 4. Reference ai_docs/ for technology details 5. Follow docs/ for deployment and testing --- *This index was last updated on 2025-01-30 with enhanced plugin implementation guides.* ## Recent Changes - Added comprehensive implementation guides to all 5 stub plugin AGENTS.md files - Each guide includes Tree-sitter integration, SQLite storage, and testing requirements - Plugin guides range from 10-12KB each with detailed code examples - Total documentation increased by ~100KB due to enhanced guides