Atomizer/docs/archive/historical/INDEX_OLD.md

Atomizer Documentation Index

Last Updated: November 21, 2025

Quick navigation to all Atomizer documentation.

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🚀 Getting Started

New Users

1. GOOD_MORNING_NOV18.md - Start here! Morning summary and quick start
2. HYBRID_MODE_GUIDE.md - Complete guide to 90% automation without API key
3. TODAY_PLAN_NOV18.md - Testing plan with step-by-step instructions

For Developers

1. DEVELOPMENT_GUIDANCE.md - Comprehensive status report and strategic direction
2. DEVELOPMENT.md - Detailed task tracking and completed work
3. DEVELOPMENT_ROADMAP.md - Long-term vision and phase-by-phase plan

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📚 Documentation by Topic

Architecture & Design

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 ⭐ 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 ⭐ 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)

• 100% natural language interaction
• Requires Claude API key
• Currently 85% complete
• Future upgrade path from Hybrid Mode

Manual Mode (Documented in ../README.md)

• Traditional JSON configuration
• 100% production ready
• Full control over every parameter

Testing & Validation

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 ⭐ 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

• Current implementation status
• Completed features (backend + live dashboard)
• Testing instructions
• Next steps (React frontend)

DASHBOARD_SESSION_SUMMARY.md

• Implementation session summary
• Features demonstrated
• How to use the dashboard
• Troubleshooting guide

../atomizer-dashboard/README.md

• Quick start guide
• API documentation
• Dashboard features overview

Recent Updates

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

• Ready-to-start summary
• Quick start instructions
• File review checklist
• Current status overview

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🗂️ By User Role

I'm an Engineer (Want to Use Atomizer)

Start Here:

1. GOOD_MORNING_NOV18.md - Overview and quick start
2. HYBRID_MODE_GUIDE.md - How to use Hybrid Mode
3. 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)

I'm a Developer (Want to Extend Atomizer)

Start Here:

1. DEVELOPMENT_GUIDANCE.md - Full status and priorities
2. ARCHITECTURE_REFACTOR_NOV17.md - New architecture
3. 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 - Comprehensive status report
2. DEVELOPMENT_ROADMAP.md - Long-term vision
3. 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

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📖 Documentation by Phase

Phase 1: Plugin System ✅ 100% Complete

• Documented in DEVELOPMENT.md
• Architecture in ../README.md

Phase 2.5-3.1: LLM Intelligence ✅ 85% Complete

• Status: DEVELOPMENT_GUIDANCE.md
• Details: DEVELOPMENT.md

Phase 3.2: Integration ⏳ Week 1 Complete

• Week 1 summary: MORNING_SUMMARY_NOV17.md
• Architecture: ARCHITECTURE_REFACTOR_NOV17.md
• User guide: HYBRID_MODE_GUIDE.md
• Testing: TODAY_PLAN_NOV18.md

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🔍 Quick Reference

Key Files

File	Purpose	Audience
GOOD_MORNING_NOV18.md	Quick start summary	Everyone
HYBRID_MODE_GUIDE.md	Complete Hybrid Mode guide	Engineers
TODAY_PLAN_NOV18.md	Testing plan	Engineers, QA
PROTOCOL_10_IMSO.md	Intelligent optimization guide	Advanced Engineers
ARCHITECTURE_REFACTOR_NOV17.md	Technical architecture	Developers
DEVELOPMENT_GUIDANCE.md	Status & priorities	Managers, Developers
DEVELOPMENT.md	Task tracking	Developers
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

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📝 Recent Changes

November 21, 2025

• Created DASHBOARD_MASTER_PLAN.md - Complete dashboard architecture
• Created DASHBOARD_IMPLEMENTATION_STATUS.md - Implementation tracking
• Created 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 - Quick start guide

November 18, 2025

• Created GOOD_MORNING_NOV18.md
• Created HYBRID_MODE_GUIDE.md
• Created TODAY_PLAN_NOV18.md
• Updated ../README.md with new doc links

November 17, 2025

• Created MORNING_SUMMARY_NOV17.md
• Created ARCHITECTURE_REFACTOR_NOV17.md
• Fixed parameter range bug
• Implemented centralized library system
• All tests passing (18/18)

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🆘 Need Help?

Common Questions

Q: How do I start using Atomizer? A: Read GOOD_MORNING_NOV18.md then follow Test 1 in TODAY_PLAN_NOV18.md

Q: What's the difference between modes? A: See comparison table in HYBRID_MODE_GUIDE.md

Q: Where is the technical architecture explained? A: ARCHITECTURE_REFACTOR_NOV17.md

Q: What's the current development status? A: DEVELOPMENT_GUIDANCE.md

Q: How do I contribute? A: Read DEVELOPMENT.md for task tracking and priorities

Troubleshooting

See troubleshooting section in:

• HYBRID_MODE_GUIDE.md
• TODAY_PLAN_NOV18.md

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📬 Contact

• Email: antoine@atomaste.com
• GitHub: Report Issues

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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 ✅