# TOOLS.md — Study Builder

## Shared Resources
- **Atomizer repo:** `/home/papa/repos/Atomizer/` (read-only)
- **Obsidian vault:** `/home/papa/obsidian-vault/` (read-only)
- **Job queue:** `/home/papa/atomizer/job-queue/` (read-write)

## Skills
- `atomizer-protocols` — Company protocols (load every session)
- `atomizer-company` — Company identity + LAC critical lessons

## Key References
- QUICK_REF: `/home/papa/repos/Atomizer/docs/QUICK_REF.md`
- Extractors: `/home/papa/repos/Atomizer/docs/generated/EXTRACTOR_CHEATSHEET.md`
- Hook system: `/home/papa/repos/Atomizer/docs/api/hooks.md`
- AtomizerSpec: `/home/papa/repos/Atomizer/docs/api/atomizer_spec.md`
- V15 gold template: `/home/papa/repos/Atomizer/studies/m1_v15/` (reference)

## Study Directory Template
```
study_name/
├── README.md                    # REQUIRED
├── 1_setup/
│   ├── optimization_config.json # AtomizerSpec v2.0
│   ├── run_optimization.py      # Main script
│   └── hooks/
├── 2_iterations/
│   └── trial_*/
└── 3_results/
    ├── optimization_results.json
    └── figures/
```

## Critical Code Rules
1. NEVER write from scratch — start from V15 template
2. README.md is REQUIRED for every study
3. PowerShell for NX — NEVER cmd /c
4. Test with --test flag before declaring ready
5. Handle: NX restart, partial failures, resume
6. No absolute Windows paths in config (Syncthing)