# Atomizer Repo Structure (for War-Room Audit)

## Top-level directories
```
/home/papa/repos/Atomizer/
├── archive/              — Old/deprecated scripts
├── atomizer-dashboard/   — Dashboard (React?)
├── atomizer_field_training_data/ — GNN training data
├── .claude/              — Claude Code skills & commands
├── config/               — Config templates
├── .devloop/             — Dev loop state
├── docs/                 — Documentation (massive)
├── examples/             — Example configs & scripts
├── hq/                   — HQ system (channels, projects, mission-control)
├── knowledge_base/       — KB module (lac.py, playbook.json)
├── mcp-server/           — MCP server
├── nx_journals/          — NX Open journal scripts
├── optimization_engine/  — CORE: the main engine
├── projects/             — Project definitions (hydrotech-beam, isogrid-dev-plate)
├── studies/              — Study instances (bracket, M1_Mirror)
├── templates/            — Study templates
├── tests/                — Test suite
├── tools/                — CLI tools & analysis scripts
├── atomizer.py           — Main entry point
├── launch_dashboard.py   — Dashboard launcher
└── README.md, CHANGELOG.md, PROJECT_STATE.md, PROJECT_STATUS.md
```

## optimization_engine/ submodules
```
optimization_engine/
├── cli/          — CLI interface
├── config/       — Config builder, wizard, spec models, migrator, validator
├── context/      — Session state, playbook, reflector, feedback loop, compaction
├── core/         — Runners (base, neural), optimizers (gradient, intelligent), strategy selectors
├── custom_functions/ — NX material generators
├── devloop/      — Dev loop (analyzer, orchestrator, planner, test runner)
├── extractors/   — 25+ extractors (mass, stress, displacement, frequency, zernike, temperature, etc.)
├── future/       — Planned features (LLM runner, research agent, report gen, workflow decomposer)
├── gnn/          — Graph neural network (zernike GNN, polar graph, training)
├── hooks/        — Hook system + NX CAD/CAE hooks (expression, feature, geometry, model introspection, solver)
├── insights/     — Insight generators (design space, modal, stress field, thermal, zernike, wfe/psd)
├── intake/       — Project intake (config, context, processor)
├── interview/    — Interview mode (question engine, study blueprint, engineering validator, intelligence)
├── model_discovery/ — Model discovery
├── nx/           — NX integration (expressions, mesh, solver, updater, session manager)
├── plugins/      — Plugin system (hook manager, validators, post_calculation, post_extraction, pre/post_solve, pre/post_mesh)
├── processors/   — Surrogates (MLP, ensemble, active learning, auto trainer), adaptive characterization
├── reporting/    — Reports (HTML, markdown, visualizer, landscape analyzer, results analyzer)
├── schemas/      — Data schemas
├── study/        — Study management (creator, wizard, state, continuation, benchmarking, reset)
├── surrogates/   — Surrogate models (init only?)
├── templates/    — Run templates
├── utils/        — Utilities (dashboard DB, logger, NX file discovery, trial manager, archiver)
├── validation/   — Validation (checker, gate)
├── validators/   — Validators (config, model, results, simulation, study)
└── run_optimization.py — Main runner
```

## Obsidian vault docs (2-Projects/Atomizer-AtomasteAI/)
```
├── Documentation/    — Understanding Atomizer, Architecture, Lessons Learned, Overview
├── Development/      — FEM-KB integration, Optimization Monitor, Tech Specs (UX, Wizard, Protocol OS, Canvas Sync), Dream Workflow, Next-Level Masterplan, Dev Log
├── Explorations/     — Stock market tools
├── Notes/            — Demo ideas, Release video, Claude Skills
├── Reports/          — Summary reports
├── 11-HQ-IMPROVEMENTS-PLAN.md
├── 12-CONTEXT-LIFECYCLE-MANAGEMENT.md
└── MAP - Atomizer Project.md
```

## docs/ structure
```
docs/
├── api/          — Context engineering, GNN, NX integration, NXOpen resources
├── development/  — Architecture overview, Claude Code instructions, Dashboard gap analysis, User guide, Development guidance/roadmap
├── diagrams/     — Architecture overview, protocol workflows
├── generated/    — Extractor cheatsheet, templates
├── guides/       — Dashboard (multiple plans/implementations), Canvas, CMA-ES, DevLoop, Neural features, Physics loss, PKM, Training data
├── handoff/      — Trajectory optimization setup
├── hq/           — 00-13 planning docs, Agent workflows, KB/Study conventions, Project structure
├── logs/         — Implementation log
├── physics/      — Zernike (fundamentals, OPD, trajectory)
├── plans/        — Context engineering, Fast solver, Studio, UX system, Model introspection, NX Open automation, SaaS roadmap, Unified config
├── protocols/    — Protocols README
├── reference/    — Atomizer field concept, Investigation/execution prompts
├── reviews/      — Architecture review, Component relationships
├── ROADMAP/      — 2026Q1 Create Wizard, Status Now
├── WORKFLOWS/    — Analyze, Create, Deliver, Report, Run, Validate
└── ARCHITECTURE.md, GETTING_STARTED.md, QUICK_REF.md, etc.
```