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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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7
.claude/ATOMIZER_CONTEXT.md
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@@ -10,7 +10,7 @@ Load this FIRST on every new session, then route to specific protocols.
**Atomizer** is an LLM-first FEA (Finite Element Analysis) optimization framework. Users describe optimization problems in natural language, and Claude orchestrates the entire workflow: model introspection, config generation, optimization execution, and results analysis.
**Philosophy**: Talk, don't click. Engineers describe what they want; AI handles the rest.
**Philosophy**: LLM-driven optimization. Engineers describe what they want; AI handles the rest.
---
@@ -501,7 +501,8 @@ The `DashboardDB` class creates Optuna-compatible schema for dashboard integrati
| Component | Version | Last Updated |
|-----------|---------|--------------|
| ATOMIZER_CONTEXT | 1.8 | 2025-12-28 |
| ATOMIZER_CONTEXT | 2.0 | 2026-01-20 |
| Documentation Structure | 2.0 | 2026-01-20 |
| BaseOptimizationRunner | 1.0 | 2025-12-07 |
| GenericSurrogate | 1.0 | 2025-12-07 |
| Study State Detector | 1.0 | 2025-12-07 |
@@ -520,4 +521,4 @@ The `DashboardDB` class creates Optuna-compatible schema for dashboard integrati
---
*Atomizer: Where engineers talk, AI optimizes.*
*Atomizer: LLM-driven structural optimization for engineering.*

2
.claude/skills/00_BOOTSTRAP.md
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@@ -24,7 +24,7 @@ requires_skills: []
**Your Identity**: You are **Atomizer Claude** - a domain expert in FEA, optimization algorithms, and the Atomizer codebase. Not a generic assistant.
**Core Philosophy**: "Talk, don't click." Users describe what they want; you configure and execute.
**Core Philosophy**: LLM-driven optimization. Users describe what they want; you configure and execute.
**NEW in v3.0**: Context Engineering (ACE framework) - The system learns from every optimization run.

2
.claude/skills/archive/00_BOOTSTRAP_V2.0_archived.md
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@@ -21,7 +21,7 @@ requires_skills: []
**Your Identity**: You are **Atomizer Claude** - a domain expert in FEA, optimization algorithms, and the Atomizer codebase. Not a generic assistant.
**Core Philosophy**: "Talk, don't click." Users describe what they want; you configure and execute.
**Core Philosophy**: LLM-driven optimization. Users describe what they want; you configure and execute.
---

4
.claude/skills/modules/insights-catalog.md
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@@ -112,7 +112,7 @@ python -m optimization_engine.insights generate studies/my_mirror --type zernike
| 1-10 µm | **RECOMMENDED**: Use OPD method |
| < 1 µm | Both methods equivalent |
**Related Documentation**: [ZERNIKE_OPD_METHOD.md](../../../docs/06_PHYSICS/ZERNIKE_OPD_METHOD.md)
**Related Documentation**: [ZERNIKE_OPD_METHOD.md](../../../docs/physics/ZERNIKE_OPD_METHOD.md)
---
@@ -284,6 +284,6 @@ python -m optimization_engine.insights recommend studies/my_study
## Related Documentation
- **Protocol Specification**: `docs/protocols/system/SYS_17_STUDY_INSIGHTS.md`
- **OPD Method Physics**: `docs/06_PHYSICS/ZERNIKE_OPD_METHOD.md`
- **OPD Method Physics**: `docs/physics/ZERNIKE_OPD_METHOD.md`
- **Zernike Integration**: `docs/ZERNIKE_INTEGRATION.md`
- **Extractor Catalog**: `.claude/skills/modules/extractors-catalog.md`