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