# ATLES Documentation Index

This is the comprehensive index of all ATLES project documentation. All documentation has been organized into logical categories for better navigation and maintenance.

## 🏗️ Architecture Documentation

| File | Description | Location |
|------|-------------|----------|
| ATLES_AUTONOMOUS_V2_DESIGN.md | Autonomous system v2 design specifications | `architecture/` |
| ATLES_CONSTITUTIONAL_SAFETY_MONITOR_DESIGN.md | Constitutional safety system design | `architecture/` |
| ATLES_TRUTH_SEEKING_SYSTEM_DESIGN.md | Truth-seeking system architecture | `architecture/` |
| Memory_Aware_Reasoning_Architecture.md | Memory-aware reasoning system design | `architecture/` |
| ATLES_Consciousness_Goals_Theory.md | Consciousness and goals theory documentation | `architecture/` |

## 🐛 Bug Reports

| File | Description | Location |
|------|-------------|----------|
| ATLES_MEMORY_SYSTEM_BUG_REPORT.md | Memory system bug analysis | `bug-reports/` |
| ATLES_MEMORY_SYNTHESIS_BUG_REPORT.md | Memory synthesis issues | `bug-reports/` |
| ATLES_MEMORY_SYNTHESIS_INCONSISTENCY_BUG_REPORT.md | Memory synthesis inconsistency issues | `bug-reports/` |

## ✅ Completion Reports

| File | Description | Location |
|------|-------------|----------|
| ATLES_AUTONOMOUS_V2_COMPLETE.md | Autonomous v2 completion status | `completion-reports/` |
| ATLES_DOCUMENT_SYSTEM_COMPLETE.md | Document system completion | `completion-reports/` |
| ATLES_SPEED_CONTROLS_COMPLETE.md | Speed controls implementation | `completion-reports/` |
| ATLES_START_STOP_CONTROLS_COMPLETE.md | Start/stop controls completion | `completion-reports/` |
| ATLES_WEIGHT_SURGERY_INTEGRATION_COMPLETE.md | Weight surgery integration status | `completion-reports/` |
| ATLES_ASYNCIO_EVENT_LOOP_FIX_COMPLETE.md | AsyncIO event loop fixes | `completion-reports/` |
| CHAT_SUBSYSTEM_FIX_COMPLETE.md | Chat subsystem fixes | `completion-reports/` |
| CORE_ARCHITECTURAL_FIX_COMPLETE.md | Core architectural fixes | `completion-reports/` |
| IDENTITY_AMNESIA_FIX_COMPLETE.md | Identity amnesia fixes | `completion-reports/` |
| UNICODE_EMOJI_FIX_COMPLETE.md | Unicode emoji fixes | `completion-reports/` |
| SOPHISTICATED_MANIPULATION_DETECTION_DEPLOYED.md | Manipulation detection deployment | `completion-reports/` |
| TRUTH_SEEKING_SYSTEM_DEPLOYED.md | Truth-seeking system deployment | `completion-reports/` |

## 📚 User Guides

| File | Description | Location |
|------|-------------|----------|
| **QWEN_MODELS_GUIDE.md** | **Complete Qwen models documentation and setup** | **`guides/`** |
| AI_CAPABILITIES_README.md | AI capabilities overview | `guides/` |
| AI_TASK_MANAGEMENT_GUIDE.md | Task management guide | `guides/` |
| CODEBASE_EXPLANATION_GUIDE.md | Codebase explanation guide | `guides/` |
| CUSTOM_MODEL_SETUP_INSTRUCTIONS.md | Custom model setup instructions | `guides/` |
| DEBUG_MODE_README.md | Debug mode documentation | `guides/` |
| DEBUG_QUICK_REFERENCE.md | Debug quick reference | `guides/` |
| DEVELOPER_GUIDE.md | Developer guide | `guides/` |
| DEPENDENCY_PDF_FEATURES.md | PDF dependency features | `guides/` |
| DEPLOY_TO_PIXEL9_GUIDE.md | Pixel 9 deployment guide | `guides/` |
| DIRECT_INSERT_GUIDE.md | Direct insert guide | `guides/` |
| ENHANCED_CONVERSATION_INTEGRATION_GUIDE.md | Enhanced conversation integration | `guides/` |
| EPISODIC_SEMANTIC_MEMORY_README.md | Episodic semantic memory guide | `guides/` |
| OLLAMA_INTEGRATION_GUIDE.md | Ollama integration guide | `guides/` |
| PDF_READING_README.md | PDF reading capabilities | `guides/` |
| PROACTIVE_MESSAGING_README.md | Proactive messaging guide | `guides/` |
| PROJECT_MANAGEMENT_GUIDE.md | Project management guide | `guides/` |
| QUICK_START_GUIDE.md | Quick start guide | `guides/` |
| REFACTORING_MIGRATION_GUIDE.md | Refactoring migration guide | `guides/` |
| SAFETY_IMPROVEMENTS_GUIDE.md | Safety improvements guide | `guides/` |
| ATLES_GLOSSARY.md | Project glossary | `guides/` |

## 🔗 Integration Documentation

| File | Description | Location |
|------|-------------|----------|
| R-ZERO_INTEGRATION_IMPLEMENTATION_SUMMARY.md | R-Zero integration summary | `integration/` |
| R-ZERO_PHASE2_IMPLEMENTATION_SUMMARY.md | R-Zero Phase 2 implementation | `integration/` |
| R-ZERO_PHASE3_IMPLEMENTATION_SUMMARY.md | R-Zero Phase 3 implementation | `integration/` |
| R-ZERO_PHASE4_IMPLEMENTATION_SUMMARY.md | R-Zero Phase 4 implementation | `integration/` |
| PROACTIVE_MESSAGING_IMPLEMENTATION_SUMMARY.md | Proactive messaging implementation | `integration/` |
| METACOG_002_IMPLEMENTATION_SUMMARY.md | Metacognitive system implementation | `integration/` |
| METACOG_003_IMPLEMENTATION_SUMMARY.md | Metacognitive system v3 implementation | `integration/` |
| CONSTITUTIONAL_FIX_IMPLEMENTATION_SUMMARY.md | Constitutional fixes implementation | `integration/` |
| INTENT_BASED_CONSTITUTIONAL_INTEGRATION_PLAN.md | Intent-based constitutional integration | `integration/` |
| ATLES_R-ZERO_INTEGRATION_PLAN.md | R-Zero integration planning | `integration/` |

## 🧠 Memory System Documentation

| File | Description | Location |
|------|-------------|----------|
| MEMORY_ARCHITECTURAL_IMPROVEMENTS_SUMMARY.md | Memory architecture improvements | `memory-system/` |
| MEMORY_ARCHITECTURE_IMPROVEMENTS.md | Memory architecture details | `memory-system/` |
| MEMORY_SYSTEM_INTEGRATION_STATUS.md | Memory system integration status | `memory-system/` |
| UNIFIED_MEMORY_INTEGRATION_SOLUTION.md | Unified memory integration solution | `memory-system/` |

## 📱 Mobile Documentation

| File | Description | Location |
|------|-------------|----------|
| ATLES_MOBILE_APP_SUMMARY.md | Mobile app summary | `mobile/` |
| ATLES_MOBILE_INTEGRATION.md | Mobile integration documentation | `mobile/` |

## 🗺️ Roadmaps

| File | Description | Location |
|------|-------------|----------|
| ATLES_ADVANCED_ROADMAP_2025.md | Advanced roadmap for 2025 | `roadmaps/` |
| ATLES_Architecture_Updates_2025.md | Architecture updates for 2025 | `roadmaps/` |

## 📊 System Analysis

| File | Description | Location |
|------|-------------|----------|
| SYSTEM_PROGRESS_ANALYSIS.md | System progress analysis | `system-analysis/` |
| ATLES_PHILOSOPHICAL_REASONING_PERFORMANCE_REPORT.md | Philosophical reasoning performance | `system-analysis/` |
| CONFIDENCE_SCORING_ANALYSIS.md | Confidence scoring analysis | `system-analysis/` |
| ROUTER_INTELLIGENCE_FIX_DOCUMENTATION.md | Router Intelligence System fix documentation | `system-analysis/` |
| ATLES_CLAUDE_PHILOSOPHICAL_CONVERSATION_LOG.md | Claude philosophical conversation log | `system-analysis/` |
| CORRECT_MODEL_HIERARCHY_SUMMARY.md | Model hierarchy summary | `system-analysis/` |

## 🧪 Testing Documentation

| File | Description | Location |
|------|-------------|----------|
| CONSTITUTIONAL_TESTING_README.md | Constitutional testing guide | `testing/` |
| TESTING_CLARIFICATION.md | Testing clarification document | `testing/` |

## 🔍 Truth Seeking Documentation

| File | Description | Location |
|------|-------------|----------|
| TRUTH_SEEKING_INTEGRATION_ANALYSIS.md | Truth-seeking integration analysis | `truth-seeking/` |
| TRUTH_SEEKING_RETRAINING_COMPLETE.md | Truth-seeking retraining completion | `truth-seeking/` |

## 📝 Updates and Status Reports

| File | Description | Location |
|------|-------------|----------|
| AUGUST_2025_RELEASE_NOTES.md | August 2025 release notes | `updates/` |
| 404_ERROR_FIX_SUMMARY.md | 404 error fix summary | `updates/` |
| 404_ERROR_PROPER_FIX_SUMMARY.md | Proper 404 error fix summary | `updates/` |
| FINAL_404_FIX_SUMMARY.md | Final 404 error fix summary | `updates/` |
| BUG_FIXES_ENABLED_SUMMARY.md | Bug fixes enabled summary | `updates/` |
| DIRECT_OLLAMA_FIX_SUMMARY.md | Direct Ollama fix summary | `updates/` |
| WEIGHT_SURGERY_INTEGRATION_STATUS.md | Weight surgery integration status | `updates/` |
| chat_8.21.2025.txt | Chat log from August 21, 2025 | `updates/` |
| chat_8.22.2025.txt | Chat log from August 22, 2025 | `updates/` |
| chat_8.24.2025.md | Chat log from August 24, 2025 | `updates/` |

## 📋 Main Documentation Files

| File | Description | Location |
|------|-------------|----------|
| ATLES_Project_Summary.md | Overall project summary | `docs/` |
| computer_vision.md | Computer vision documentation | `docs/` |

## 🔍 Search Tips

- **Architecture**: Look in `architecture/` for system design documents
- **Bug Reports**: Check `bug-reports/` for known issues and fixes
- **Guides**: Visit `guides/` for user and developer documentation
- **Integration**: See `integration/` for system integration details
- **Memory**: Review `memory-system/` for memory-related documentation
- **Mobile**: Check `mobile/` for mobile app documentation
- **Roadmaps**: Look in `roadmaps/` for project planning
- **Analysis**: Visit `system-analysis/` for performance and analysis reports
- **Testing**: See `testing/` for testing documentation
- **Truth Seeking**: Check `truth-seeking/` for truth-seeking system docs
- **Updates**: Visit `updates/` for latest fixes and release notes

## 📅 Last Updated
September 12, 2025 - Complete documentation reorganization

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*This index provides a comprehensive overview of all ATLES documentation organized by category for easy navigation and maintenance.*