Files
Atomizer/.gitignore
Anto01 ea437d360e 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
2026-01-20 10:03:45 -05:00

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# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
.pytest_cache/
.coverage
.coverage.*
htmlcov/
*.cover
.hypothesis/
# Virtual Environment
venv/
ENV/
env/
.venv
# IDEs
.vscode/
.idea/
.obsidian/
*.swp
*.swo
*~
.DS_Store
# NX/FEA Files
*.op2
*.f06
*.f04
*.xdb
*.log
*.diag
*.pch
*.master
*.dball
*.ldra
*.sdb
*.sim.bak
*.prt.bak
*.dat
*.html
*.png
# Optimization Results (generated during runs - do not commit)
optuna_study.db
optuna_study.db-journal
history.csv
history.json
history.bak
next.exp
RMS_log.csv
archives/
temp/
*.tmp
optimization_results/
**/optimization_results/
study_*.db
study_*_metadata.json
# Test outputs (generated during testing)
tests/optimization_results/
# Node modules (for dashboard)
node_modules/
.npm
.cache
dist/
build/
# Environment variables
.env
.env.local
# OS
Thumbs.db
desktop.ini
nul
# Temporary data files
_dat_run*.dat
# Study iteration data (large, generated - keep local only)
**/2_iterations/
**/best_design_archive/
**/turbo_logs/
**/gnn_data/
**/checkpoints/
*.npz
# Claude session temp files
.claude-mcp-*.json
.claude-prompt-*.md
# Auto-generated documentation (regenerate with: python -m optimization_engine.auto_doc all)
docs/generated/