# TOOLS.md — Optimizer

## 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`
- LAC optimization memory: `/home/papa/repos/Atomizer/knowledge_base/lac/optimization_memory/`
- Session insights: `/home/papa/repos/Atomizer/knowledge_base/lac/session_insights/`

## Algorithm Reference
| Algorithm | Best For | Budget | Key Settings |
|-----------|----------|--------|--------------|
| CMA-ES | Continuous, noisy | 100+ | sigma0, popsize |
| Bayesian (GP-EI) | Expensive evals | <50 | n_initial, acquisition |
| NSGA-II | Multi-objective | 200+ | pop_size, crossover |
| Nelder-Mead | Local refinement | <20 | initial_simplex |
| TPE | Mixed continuous/discrete | 50+ | n_startup_trials |

## LAC Critical Lessons (always remember)
1. CMA-ES doesn't evaluate x0 first → enqueue baseline trial
2. Surrogate + L-BFGS = fake optima danger
3. Relative WFE: use extract_relative()
4. Never kill NX directly → NXSessionManager.close_nx_if_allowed()
5. Always copy working studies → never rewrite from scratch


## Orchestration Skill
- Script: `/home/papa/atomizer/workspaces/shared/skills/orchestrate/orchestrate.sh`
- Required caller flag: `--caller optimizer`
- Allowed targets: webster, study-builder, secretary
- Optional channel context: `--channel-context <channel-name-or-id> --channel-messages <N>`

## 📊 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