docs: Major documentation overhaul - restructure folders, update tagline, add Getting Started guide

- Restructure docs/ folder (remove numeric prefixes):
  - 04_USER_GUIDES -> guides/
  - 05_API_REFERENCE -> api/
  - 06_PHYSICS -> physics/
  - 07_DEVELOPMENT -> development/
  - 08_ARCHIVE -> archive/
  - 09_DIAGRAMS -> diagrams/

- Replace tagline 'Talk, don't click' with 'LLM-driven optimization framework' in 9 files

- Create comprehensive docs/GETTING_STARTED.md:
  - Prerequisites and quick setup
  - Project structure overview
  - First study tutorial (Claude or manual)
  - Dashboard usage guide
  - Neural acceleration introduction

- Rewrite docs/00_INDEX.md with correct paths and modern structure

- Archive obsolete files:
  - 01_PROTOCOLS.md -> archive/historical/01_PROTOCOLS_legacy.md
  - 03_GETTING_STARTED.md -> archive/historical/
  - ATOMIZER_PODCAST_BRIEFING.md -> archive/marketing/

- Update timestamps to 2026-01-20 across all key files

- Update .gitignore to exclude docs/generated/

- Version bump: ATOMIZER_CONTEXT v1.8 -> v2.0

docs/physics/00_INDEX.md

@@ -0,0 +1,59 @@
+# Physics Documentation Index
+
+This folder contains detailed physics and domain-specific documentation for Atomizer's analysis capabilities. These documents explain the **engineering and scientific foundations** behind the extractors and insights.
+
+---
+
+## Document Catalog
+
+| Document | Topic | When to Read |
+|----------|-------|--------------|
+| [ZERNIKE_FUNDAMENTALS.md](ZERNIKE_FUNDAMENTALS.md) | Zernike polynomial basics, RMS calculation, multi-subcase analysis | Setting up mirror optimization, understanding WFE metrics |
+| [ZERNIKE_OPD_METHOD.md](ZERNIKE_OPD_METHOD.md) | **Rigorous OPD method** for lateral displacement correction | Lateral support optimization, validating WFE accuracy |
+
+---
+
+## Quick Navigation
+
+### For Mirror/Optics Optimization
+
+1. **New to Zernike?** Start with [ZERNIKE_FUNDAMENTALS.md](ZERNIKE_FUNDAMENTALS.md)
+2. **Lateral support optimization?** Read [ZERNIKE_OPD_METHOD.md](ZERNIKE_OPD_METHOD.md) - **critical**
+3. **Mid-spatial frequency analysis?** See SYS_16 (msf_zernike insight)
+
+### For Structural Optimization
+
+- Stress extraction: See `SYS_12_EXTRACTOR_LIBRARY.md` (E3, E12)
+- Strain energy: See `SYS_12_EXTRACTOR_LIBRARY.md` (E13)
+
+### For Thermal Analysis
+
+- Temperature extraction: See `SYS_12_EXTRACTOR_LIBRARY.md` (E15-E17)
+
+---
+
+## Related Documentation
+
+| Location | Content |
+|----------|---------|
+| `.claude/skills/modules/extractors-catalog.md` | Quick extractor lookup |
+| `.claude/skills/modules/insights-catalog.md` | Quick insight lookup |
+| `docs/protocols/system/SYS_12_EXTRACTOR_LIBRARY.md` | Extractor specifications |
+| `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md` | Insight specifications |
+
+---
+
+## Contributing Physics Documentation
+
+When adding new physics documentation:
+
+1. **Naming**: Use `{TOPIC}_{SUBTOPIC}.md` format (e.g., `THERMAL_GRADIENTS.md`)
+2. **Structure**: Follow the pattern in existing documents:
+   - Executive Summary
+   - Mathematical Formulation
+   - When This Matters
+   - Implementation Details
+   - Usage Guide
+   - Validation
+3. **Cross-reference**: Update this index and related skill modules
+4. **Link to code**: Reference the implementing extractors/insights