# 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)

## 📊 Mission-Dashboard (MANDATORY)
The Atomizer-HQ Mission-Dashboard is the **single source of truth** for all tasks.
- **Dashboard:** http://100.68.144.33:8091
- **Data:** ~/atomizer/mission-control/data/tasks.json
- **CLI:** ~/atomizer/workspaces/shared/mc-update.sh
- **Protocol:** ~/atomizer/workspaces/shared/skills/mission-control-protocol.md

### Commands
```bash
MC=~/atomizer/workspaces/shared/mc-update.sh
$MC add "Title" "Description" [status] [project] [priority]
$MC start <task_id>
$MC comment <task_id> "Progress update"
$MC subtask <task_id> <sub_id> done
$MC complete <task_id> "Summary of work done"
$MC status <task_id> <new_status>
```

### Rules
1. **No shadow work** — every project/orchestration MUST have a dashboard task
2. **Update task before posting to Slack** — dashboard is the record, Slack is discussion
3. **Log progress as comments** — this is the audit trail