# Atomizer Documentation Index

**Last Updated**: November 21, 2025

Quick navigation to all Atomizer documentation.

---

## 🚀 Getting Started

### New Users
1. **[GOOD_MORNING_NOV18.md](../GOOD_MORNING_NOV18.md)** - Start here! Morning summary and quick start
2. **[HYBRID_MODE_GUIDE.md](HYBRID_MODE_GUIDE.md)** - Complete guide to 90% automation without API key
3. **[TODAY_PLAN_NOV18.md](TODAY_PLAN_NOV18.md)** - Testing plan with step-by-step instructions

### For Developers
1. **[DEVELOPMENT_GUIDANCE.md](../DEVELOPMENT_GUIDANCE.md)** - Comprehensive status report and strategic direction
2. **[DEVELOPMENT.md](../DEVELOPMENT.md)** - Detailed task tracking and completed work
3. **[DEVELOPMENT_ROADMAP.md](../DEVELOPMENT_ROADMAP.md)** - Long-term vision and phase-by-phase plan

---

## 📚 Documentation by Topic

### Architecture & Design

**[ARCHITECTURE_REFACTOR_NOV17.md](ARCHITECTURE_REFACTOR_NOV17.md)**
- Centralized library system explained
- Before/after architecture comparison
- Migration guide
- Implementation details
- 400+ lines of comprehensive technical documentation

**[PROTOCOL_10_IMSO.md](PROTOCOL_10_IMSO.md)** ⭐ **Advanced**
- Intelligent Multi-Strategy Optimization
- Adaptive characterization phase
- Automatic algorithm selection (GP-BO, CMA-ES, TPE)
- Two-study architecture explained
- 41% reduction in trials vs TPE alone

### Operation Modes

**[HYBRID_MODE_GUIDE.md](HYBRID_MODE_GUIDE.md)** ⭐ **Recommended**
- What is Hybrid Mode (90% automation)
- Step-by-step workflow
- Real examples with code
- Troubleshooting guide
- Tips for success
- No API key required!

**Full LLM Mode** (Documented in [DEVELOPMENT_GUIDANCE.md](../DEVELOPMENT_GUIDANCE.md))
- 100% natural language interaction
- Requires Claude API key
- Currently 85% complete
- Future upgrade path from Hybrid Mode

**Manual Mode** (Documented in [../README.md](../README.md))
- Traditional JSON configuration
- 100% production ready
- Full control over every parameter

### Testing & Validation

**[TODAY_PLAN_NOV18.md](TODAY_PLAN_NOV18.md)**
- 4 comprehensive tests (2-3 hours)
- Test 1: Verify beam optimization (30 min)
- Test 2: Create new optimization (1 hour)
- Test 3: Validate deduplication (15 min)
- Test 4: Dashboard visualization (30 min - optional)

### Dashboard & Monitoring

**[DASHBOARD_MASTER_PLAN.md](DASHBOARD_MASTER_PLAN.md)** ⭐ **New**
- Complete dashboard architecture
- 3-page dashboard system (Configurator, Live Dashboard, Results Viewer)
- Tech stack recommendations (FastAPI + React + WebSocket)
- Implementation phases
- WebSocket protocol specification

**[DASHBOARD_IMPLEMENTATION_STATUS.md](DASHBOARD_IMPLEMENTATION_STATUS.md)**
- Current implementation status
- Completed features (backend + live dashboard)
- Testing instructions
- Next steps (React frontend)

**[DASHBOARD_SESSION_SUMMARY.md](DASHBOARD_SESSION_SUMMARY.md)**
- Implementation session summary
- Features demonstrated
- How to use the dashboard
- Troubleshooting guide

**[../atomizer-dashboard/README.md](../atomizer-dashboard/README.md)**
- Quick start guide
- API documentation
- Dashboard features overview

### Recent Updates

**[MORNING_SUMMARY_NOV17.md](../MORNING_SUMMARY_NOV17.md)**
- Critical bugs fixed (parameter ranges)
- Major architecture refactor
- New components created
- Test results (18/18 checks passing)

**[GOOD_MORNING_NOV18.md](../GOOD_MORNING_NOV18.md)**
- Ready-to-start summary
- Quick start instructions
- File review checklist
- Current status overview

---

## 🗂️ By User Role

### I'm an Engineer (Want to Use Atomizer)

**Start Here**:
1. [GOOD_MORNING_NOV18.md](../GOOD_MORNING_NOV18.md) - Overview and quick start
2. [HYBRID_MODE_GUIDE.md](HYBRID_MODE_GUIDE.md) - How to use Hybrid Mode
3. [TODAY_PLAN_NOV18.md](TODAY_PLAN_NOV18.md) - Try Test 1 to verify system

**Then**:
- Run your first optimization with Hybrid Mode
- Review beam optimization example
- Ask Claude to create workflow JSON for your problem
- Monitor live with the dashboard ([../atomizer-dashboard/README.md](../atomizer-dashboard/README.md))

### I'm a Developer (Want to Extend Atomizer)

**Start Here**:
1. [DEVELOPMENT_GUIDANCE.md](../DEVELOPMENT_GUIDANCE.md) - Full status and priorities
2. [ARCHITECTURE_REFACTOR_NOV17.md](ARCHITECTURE_REFACTOR_NOV17.md) - New architecture
3. [DEVELOPMENT.md](../DEVELOPMENT.md) - Task tracking

**Then**:
- Review core library system code
- Check extractor_library.py implementation
- Read migration guide for adding new extractors

### I'm Managing the Project (Want Big Picture)

**Start Here**:
1. [DEVELOPMENT_GUIDANCE.md](../DEVELOPMENT_GUIDANCE.md) - Comprehensive status report
2. [DEVELOPMENT_ROADMAP.md](../DEVELOPMENT_ROADMAP.md) - Long-term vision
3. [MORNING_SUMMARY_NOV17.md](../MORNING_SUMMARY_NOV17.md) - Recent progress

**Key Metrics**:
- Overall completion: 85-90%
- Phase 3.2 Week 1: 100% complete
- All tests passing (18/18)
- Production-grade architecture achieved

---

## 📖 Documentation by Phase

### Phase 1: Plugin System ✅ 100% Complete
- Documented in [DEVELOPMENT.md](../DEVELOPMENT.md)
- Architecture in [../README.md](../README.md)

### Phase 2.5-3.1: LLM Intelligence ✅ 85% Complete
- Status: [DEVELOPMENT_GUIDANCE.md](../DEVELOPMENT_GUIDANCE.md)
- Details: [DEVELOPMENT.md](../DEVELOPMENT.md)

### Phase 3.2: Integration ⏳ Week 1 Complete
- Week 1 summary: [MORNING_SUMMARY_NOV17.md](../MORNING_SUMMARY_NOV17.md)
- Architecture: [ARCHITECTURE_REFACTOR_NOV17.md](ARCHITECTURE_REFACTOR_NOV17.md)
- User guide: [HYBRID_MODE_GUIDE.md](HYBRID_MODE_GUIDE.md)
- Testing: [TODAY_PLAN_NOV18.md](TODAY_PLAN_NOV18.md)

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## 🔍 Quick Reference

### Key Files

| File | Purpose | Audience |
|------|---------|----------|
| [GOOD_MORNING_NOV18.md](../GOOD_MORNING_NOV18.md) | Quick start summary | Everyone |
| [HYBRID_MODE_GUIDE.md](HYBRID_MODE_GUIDE.md) | Complete Hybrid Mode guide | Engineers |
| [TODAY_PLAN_NOV18.md](TODAY_PLAN_NOV18.md) | Testing plan | Engineers, QA |
| [PROTOCOL_10_IMSO.md](PROTOCOL_10_IMSO.md) | Intelligent optimization guide | Advanced Engineers |
| [ARCHITECTURE_REFACTOR_NOV17.md](ARCHITECTURE_REFACTOR_NOV17.md) | Technical architecture | Developers |
| [DEVELOPMENT_GUIDANCE.md](../DEVELOPMENT_GUIDANCE.md) | Status & priorities | Managers, Developers |
| [DEVELOPMENT.md](../DEVELOPMENT.md) | Task tracking | Developers |
| [DEVELOPMENT_ROADMAP.md](../DEVELOPMENT_ROADMAP.md) | Long-term vision | Managers |

### Key Concepts

**Hybrid Mode** (90% automation)
- You describe optimization to Claude
- Claude creates workflow JSON
- LLMOptimizationRunner does the rest
- No API key required
- Production ready

**Centralized Library**
- Core extractors in `optimization_engine/extractors/`
- Study folders only contain references
- Signature-based deduplication
- Code reuse across all studies
- Clean professional structure

**Study Folder Structure**
```
studies/my_optimization/
├── extractors_manifest.json       # References to core library
├── llm_workflow_config.json        # What LLM understood
├── optimization_results.json       # Best design found
└── optimization_history.json       # All trials
```

---

## 📝 Recent Changes

### November 21, 2025
- Created [DASHBOARD_MASTER_PLAN.md](DASHBOARD_MASTER_PLAN.md) - Complete dashboard architecture
- Created [DASHBOARD_IMPLEMENTATION_STATUS.md](DASHBOARD_IMPLEMENTATION_STATUS.md) - Implementation tracking
- Created [DASHBOARD_SESSION_SUMMARY.md](DASHBOARD_SESSION_SUMMARY.md) - Session summary
- Implemented FastAPI backend with WebSocket streaming
- Built live dashboard with Chart.js (convergence + parameter space plots)
- Added pruning alerts and data export (JSON/CSV)
- Created [../atomizer-dashboard/README.md](../atomizer-dashboard/README.md) - Quick start guide

### November 18, 2025
- Created [GOOD_MORNING_NOV18.md](../GOOD_MORNING_NOV18.md)
- Created [HYBRID_MODE_GUIDE.md](HYBRID_MODE_GUIDE.md)
- Created [TODAY_PLAN_NOV18.md](TODAY_PLAN_NOV18.md)
- Updated [../README.md](../README.md) with new doc links

### November 17, 2025
- Created [MORNING_SUMMARY_NOV17.md](../MORNING_SUMMARY_NOV17.md)
- Created [ARCHITECTURE_REFACTOR_NOV17.md](ARCHITECTURE_REFACTOR_NOV17.md)
- Fixed parameter range bug
- Implemented centralized library system
- All tests passing (18/18)

---

## 🆘 Need Help?

### Common Questions

**Q: How do I start using Atomizer?**
A: Read [GOOD_MORNING_NOV18.md](../GOOD_MORNING_NOV18.md) then follow Test 1 in [TODAY_PLAN_NOV18.md](TODAY_PLAN_NOV18.md)

**Q: What's the difference between modes?**
A: See comparison table in [HYBRID_MODE_GUIDE.md](HYBRID_MODE_GUIDE.md#comparison-three-modes)

**Q: Where is the technical architecture explained?**
A: [ARCHITECTURE_REFACTOR_NOV17.md](ARCHITECTURE_REFACTOR_NOV17.md)

**Q: What's the current development status?**
A: [DEVELOPMENT_GUIDANCE.md](../DEVELOPMENT_GUIDANCE.md)

**Q: How do I contribute?**
A: Read [DEVELOPMENT.md](../DEVELOPMENT.md) for task tracking and priorities

### Troubleshooting

See troubleshooting section in:
- [HYBRID_MODE_GUIDE.md](HYBRID_MODE_GUIDE.md#troubleshooting)
- [TODAY_PLAN_NOV18.md](TODAY_PLAN_NOV18.md#if-something-fails)

---

## 📬 Contact

- **Email**: antoine@atomaste.com
- **GitHub**: [Report Issues](https://github.com/yourusername/Atomizer/issues)

---

**Last Updated**: November 21, 2025
**Atomizer Version**: Phase 3.2 Week 1 Complete + Live Dashboard ✅ (85-90% overall)
**Documentation Status**: Comprehensive and up-to-date ✅
