# Code-Index-MCP Documentation Table of Contents
Generated: 2025-01-30
## Executive Summary
### Project Overview
- **Project**: Code-Index-MCP - Local-first code indexer with MCP (Model Context Protocol) support
- **Complexity**: 5/5 (High - 136k lines, 48 language plugins, semantic search)
- **Implementation Status**: 95% complete (100% features, 83% MCP sub-agent failure)
- **Architecture Alignment**: 85% (Strong alignment between design and implementation)
- **Documentation Files**: 141+ markdown files across multiple categories
### Critical Issues
1. **MCP Sub-Agent Tool Inheritance**: 83% failure rate - Task agents cannot access MCP tools
2. **Index Path Discovery**: Limited to single path, missing test repository indexes
3. **Documentation Migration**: Multiple CLAUDE.md files need migration to AGENTS.md pattern
4. **Architecture Updates**: Some PlantUML diagrams need updates to reflect latest implementations
## Documentation Architecture
### 1. AI Agent Context Files (20 files)
#### Primary Agent Instructions
| File | Purpose | Status | Complexity | Migration Needed |
|------|---------|--------|------------|------------------|
| `/CLAUDE.md` | Main entry (stub) | ACTIVE | 1/5 | Points to AGENTS.md ✅ |
| `/AGENTS.md` | Primary configuration | ACTIVE | 5/5 | Current main file |
| `/ROADMAP.md` | Development roadmap | ACTIVE | 5/5 | 95% complete, MCP issues documented |
#### Architecture Agent Files
| File | Purpose | Status | Complexity | Migration Needed |
|------|---------|--------|------------|------------------|
| `/architecture/CLAUDE.md` | Architecture stub | STUB | 1/5 | Points to AGENTS.md ✅ |
| `/architecture/AGENTS.md` | C4 model guidance | ACTIVE | 3/5 | Current, no migration |
#### Plugin Agent Files
| Directory | CLAUDE.md | AGENTS.md | Status | Notes |
|-----------|-----------|-----------|--------|-------|
| python_plugin | ✅ Stub | ✅ Active | MIGRATED | Only fully implemented plugin |
| js_plugin | ✅ Stub | ✅ Active | MIGRATED | Enhanced implementation |
| c_plugin | ✅ Stub | ✅ Active | MIGRATED | Tree-sitter integration |
| cpp_plugin | ✅ Stub | ✅ Active | MIGRATED | Template support |
| dart_plugin | ✅ Stub | ✅ Active | MIGRATED | Flutter support |
| html_css_plugin | ✅ Stub | ✅ Active | MIGRATED | Selector analysis |
| java_plugin | ✅ Active | ✅ Active | NEEDS REVIEW | Both files active |
### 2. C4 Architecture Files (44 files)
#### Structurizr DSL
| File | Level | Status | Alignment | Complexity |
|------|-------|--------|-----------|------------|
| `/architecture/workspace.dsl` | All | ACTIVE | 95% aligned | 5/5 |
#### PlantUML Level 4 Diagrams
| Category | Files | Status | Notes |
|----------|-------|--------|-------|
| Core Components | 10 | ALIGNED | dispatcher.puml, plugin_factory.puml, etc. |
| Language Plugins | 15 | ALIGNED | All plugins have diagrams |
| Storage & Index | 5 | ALIGNED | storage_actual.puml, index_management.puml |
| MCP Issues | 3 | NEW | Sub-agent architecture diagrams |
| Document Processing | 4 | ALIGNED | markdown_plugin.puml, plaintext_plugin.puml |
### 3. Implementation Documentation (77 files)
#### Core Documentation
| Category | Files | Purpose | Complexity |
|----------|-------|---------|------------|
| `/docs/` | 25 | Main documentation | 2-4/5 |
| `/docs/implementation/` | 18 | Implementation details | 3-5/5 |
| `/docs/status/` | 20 | Status reports | 2-3/5 |
| `/docs/reports/` | 10 | Test and analysis reports | 3-4/5 |
#### Critical Implementation Files
| File | Purpose | Complexity | Key Information |
|------|---------|------------|------------------|
| `PROJECT_COMPLETION_SUMMARY.md` | Overall status | 5/5 | 95% complete |
| `MCP_VERIFICATION_IMPLEMENTATION_SUMMARY.md` | MCP testing | 5/5 | 83% failure documented |
| `PATH_MANAGEMENT_IMPLEMENTATION_SUMMARY.md` | Path handling | 5/5 | Relative paths complete |
| `INDEX_MANAGEMENT_SUMMARY.md` | Index storage | 4/5 | Local .indexes/ structure |
### 4. Framework Documentation (`/ai_docs/` - 22 files)
#### Coverage Assessment
| Framework | File | Status | Staleness | Used in Project |
|-----------|------|--------|-----------|------------------|
| FastAPI | `fastapi_overview.md` | CURRENT | Low | ✅ Primary API |
| Tree-sitter | `tree_sitter_overview.md` | CURRENT | Low | ✅ Core parsing |
| Qdrant | `qdrant.md` | CURRENT | Low | ✅ Vector storage |
| Voyage AI | `voyage_ai_overview.md` | CURRENT | Low | ✅ Embeddings |
| SQLite FTS5 | `sqlite_fts5_overview.md` | CURRENT | Low | ✅ Text search |
| Redis | `redis.md` | STALE | High | ❌ Not implemented |
| Celery | `celery_overview.md` | STALE | High | ❌ Not implemented |
| gRPC | `grpc_overview.md` | STALE | High | ❌ Not implemented |
| Memgraph | `memgraph_overview.md` | STALE | High | ❌ Not implemented |
### 5. Roadmap Implementation Analysis
#### Completion Status by Category
| Category | Items | Complete | In Progress | Not Started | Complexity |
|----------|-------|----------|-------------|-------------|------------|
| Core System | 20 | 20 (100%) | 0 | 0 | 3-5/5 |
| Language Plugins | 48 | 48 (100%) | 0 | 0 | 2-4/5 |
| Advanced Features | 10 | 10 (100%) | 0 | 0 | 4-5/5 |
| MCP Infrastructure | 4 | 0 | 0 | 4 (0%) | 5/5 |
| Future Enhancements | 8 | 0 | 0 | 8 | 3-4/5 |
#### Critical Blockers (from ROADMAP.md)
1. **MCP Sub-Agent Tool Inheritance** [Complexity: 5/5] 🔴 BLOCKING
- 83% failure rate in production environments
- Task agents don't inherit parent MCP configuration
- Prevents production deployment with MCP
2. **Multi-Path Index Discovery** [Complexity: 4/5] 🔴 BLOCKING
- Only checks `.indexes/` path
- Misses test repository indexes
- Causes 0% success for some languages
### 6. Codebase-Architecture Divergences
#### Aligned Components (85%)
| Component | Architecture | Implementation | Status |
|-----------|--------------|----------------|--------|
| Plugin System | ✅ workspace.dsl | ✅ 48 plugins | ALIGNED |
| Dispatcher | ✅ Enhanced design | ✅ Timeout + bypass | ALIGNED |
| Storage | ✅ SQLite + Qdrant | ✅ Local .indexes/ | ALIGNED |
| API Gateway | ✅ FastAPI design | ✅ All endpoints | ALIGNED |
#### Divergences Identified (15%)
| Issue | Architecture | Reality | Impact |
|-------|--------------|---------|--------|
| Sub-Agent Support | Not designed | 83% failure | CRITICAL |
| Index Discovery | Single path | Need multi-path | HIGH |
| Performance Metrics | Designed | Not published | MEDIUM |
| Some PlantUML | Outdated | Need updates | LOW |
### 7. AI Platform Guidance Consistency
#### Consistency Analysis
| Aspect | AGENTS.md | CLAUDE.md | Architecture | Status |
|--------|-----------|-----------|--------------|--------|
| MCP-First Search | ✅ Emphasized | ✅ Redirects | ✅ Designed | CONSISTENT |
| Implementation Status | 100% claimed | N/A | 95% actual | NEEDS UPDATE |
| Critical Issues | ✅ Documented | N/A | ✅ In diagrams | CONSISTENT |
| Tool Priority | ✅ Clear order | N/A | ✅ Reflected | CONSISTENT |
## Recommendations
### 1. Immediate Actions (Week 1)
1. **Fix MCP Sub-Agent Inheritance** - Update architecture to handle tool propagation
2. **Implement Multi-Path Discovery** - Add fallback paths for index location
3. **Update AGENTS.md** - Adjust 100% claim to reflect 95% reality
4. **Publish Performance Metrics** - Complete missing benchmark documentation
### 2. Documentation Cleanup (Week 2)
1. **Consolidate Status Reports** - Move older reports to archives
2. **Remove Stale ai_docs** - Archive unused framework documentation
3. **Update PlantUML Diagrams** - Sync with latest implementations
4. **Create MCP Troubleshooting Guide** - Document known issues and workarounds
### 3. Architecture Alignment (Week 3)
1. **Update workspace.dsl** - Add sub-agent architecture components
2. **Create New Diagrams** - Document MCP configuration flow
3. **Review Plugin Documentation** - Ensure all reflect current state
4. **Document Index Management** - Comprehensive guide for .indexes/ structure
## Navigation Guide
### For AI Agents
1. Start with `/AGENTS.md` for current state and capabilities
2. Check `/ROADMAP.md` for implementation priorities
3. Use MCP tools when available (17% success rate)
4. Fall back to native tools (90% success rate)
5. Review architecture files for system design
### For Humans
1. Begin with `/docs/PROJECT_STRUCTURE.md` for overview
2. Check `/docs/DEPLOYMENT-GUIDE.md` for setup
3. Review `/docs/status/` for current state
4. Use `/docs/TROUBLESHOOTING.md` for issues
5. See `/architecture/` for system design
## Appendix: File Size Analysis
### Largest Documentation Files
1. `/ai_docs/qdrant.md` - 50.9KB (Vector database guide)
2. `/ROADMAP.md` - 35.8KB (Complete development roadmap)
3. `/docs/implementation/PROJECT_COMPLETION_SUMMARY.md` - 28.4KB
4. `/ai_docs/fastapi_overview.md` - 25.1KB (API framework guide)
5. `/ai_docs/tree_sitter_overview.md` - 23.7KB (Parser guide)
### Documentation Categories by Size
| Category | Files | Total Size | Avg Size |
|----------|-------|------------|----------|
| Implementation Reports | 45 | ~450KB | 10KB |
| AI Framework Guides | 22 | ~350KB | 16KB |
| Architecture Files | 44 | ~250KB | 5.7KB |
| Status Reports | 20 | ~200KB | 10KB |
| Agent Instructions | 20 | ~150KB | 7.5KB |
## Metadata
- **Generated**: 2025-01-30
- **Total Files Analyzed**: 141+ markdown files
- **Analysis Complexity**: Comprehensive with architectural alignment
- **Next Update**: When MCP issues are resolved or major changes occur
