chore(hq): daily sync 2026-02-21

hq/workspaces/shared/war-room-overhaul/repo-structure.md

@@ -0,0 +1,91 @@
+# 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.
+```