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

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- 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
This commit is contained in:
Anto01
2026-01-20 10:03:45 -05:00
parent 37f73cc2be
commit ea437d360e
103 changed files with 8980 additions and 327 deletions
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8
studies/M1_Mirror/README.md
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@@ -249,7 +249,7 @@ V6 (TPE) → V7 (CMA-ES whiffle) → V8 (CMA-ES lateral) → V9 (CMA-ES co
> **Important**: `abs(RMS_target - RMS_ref)` is WRONG. Always use `extract_relative()` for relative metrics.
See: [docs/06_PHYSICS/ZERNIKE_OPD_METHOD.md](../../docs/06_PHYSICS/ZERNIKE_OPD_METHOD.md)
See: [docs/physics/ZERNIKE_OPD_METHOD.md](../../docs/physics/ZERNIKE_OPD_METHOD.md)
### 8.2 WFE Convention
@@ -323,12 +323,12 @@ python -m optimization_engine.insights generate . --type zernike_opd_comparison
| Document | Description |
|----------|-------------|
| [M1_MIRROR_CAMPAIGN_SUMMARY.md](m1_mirror_adaptive_V15/M1_MIRROR_CAMPAIGN_SUMMARY.md) | V11-V15 campaign analysis |
| [docs/06_PHYSICS/ZERNIKE_FUNDAMENTALS.md](../../docs/06_PHYSICS/ZERNIKE_FUNDAMENTALS.md) | Zernike analysis basics |
| [docs/06_PHYSICS/ZERNIKE_OPD_METHOD.md](../../docs/06_PHYSICS/ZERNIKE_OPD_METHOD.md) | OPD method for lateral supports |
| [docs/physics/ZERNIKE_FUNDAMENTALS.md](../../docs/physics/ZERNIKE_FUNDAMENTALS.md) | Zernike analysis basics |
| [docs/physics/ZERNIKE_OPD_METHOD.md](../../docs/physics/ZERNIKE_OPD_METHOD.md) | OPD method for lateral supports |
| [.claude/skills/modules/extractors-catalog.md](../../.claude/skills/modules/extractors-catalog.md) | Extractor quick reference |
---
*M1 Mirror Optimization Project*
*Atomizer Framework*
*Last Updated: 2025-12-23*
*Last Updated: 2026-01-20*