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docs: Major documentation overhaul - restructure folders, update tagline, add Getting Started guide

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- Restructure docs/ folder (remove numeric prefixes):
  - 04_USER_GUIDES -> guides/
  - 05_API_REFERENCE -> api/
  - 06_PHYSICS -> physics/
  - 07_DEVELOPMENT -> development/
  - 08_ARCHIVE -> archive/
  - 09_DIAGRAMS -> diagrams/

- Replace tagline 'Talk, don't click' with 'LLM-driven optimization framework' in 9 files

- Create comprehensive docs/GETTING_STARTED.md:
  - Prerequisites and quick setup
  - Project structure overview
  - First study tutorial (Claude or manual)
  - Dashboard usage guide
  - Neural acceleration introduction

- Rewrite docs/00_INDEX.md with correct paths and modern structure

- Archive obsolete files:
  - 01_PROTOCOLS.md -> archive/historical/01_PROTOCOLS_legacy.md
  - 03_GETTING_STARTED.md -> archive/historical/
  - ATOMIZER_PODCAST_BRIEFING.md -> archive/marketing/

- Update timestamps to 2026-01-20 across all key files

- Update .gitignore to exclude docs/generated/

- Version bump: ATOMIZER_CONTEXT v1.8 -> v2.0
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Anto01
2026-01-20 10:03:45 -05:00
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# Dashboard Implementation Status
**Last Updated**: January 16, 2026
**Version**: 3.0
---
## Overview
The Atomizer Dashboard V2 is now feature-complete with the Canvas Builder. This document tracks implementation status across all major features.
---
## Phase Summary
| Phase | Name | Status | Notes |
|-------|------|--------|-------|
| 0 | MCP Chat Foundation | COMPLETE | Claude API integration, session management |
| 1 | Canvas with React Flow | COMPLETE | 8 node types, validation, serialization |
| 2 | LLM Intelligence Layer | COMPLETE | Canvas chat hook, MCP canvas tools |
| 3 | Bidirectional Sync | COMPLETE | Session persistence, context builder |
| 4 | Templates & Polish | COMPLETE | Template selector, config importer |
| 5 | Tauri Desktop | PLANNED | Future phase |
---
## Phase 0: MCP Chat Foundation - COMPLETE
### Backend Services
| Component | File | Lines | Status |
|-----------|------|-------|--------|
| Claude Agent | `backend/api/services/claude_agent.py` | 722 | COMPLETE |
| CLI Agent | `backend/api/services/claude_cli_agent.py` | 202 | COMPLETE |
| Conversation Store | `backend/api/services/conversation_store.py` | 295 | COMPLETE |
| Session Manager | `backend/api/services/session_manager.py` | 425 | COMPLETE |
| Context Builder | `backend/api/services/context_builder.py` | 246 | COMPLETE |
### MCP Server
| Tool | Description | Status |
|------|-------------|--------|
| `list_studies` | List all studies | COMPLETE |
| `get_study_status` | Study details | COMPLETE |
| `create_study` | Create from description | COMPLETE |
| `run_optimization` | Start optimization | COMPLETE |
| `stop_optimization` | Stop optimization | COMPLETE |
| `get_trial_data` | Query trials | COMPLETE |
| `analyze_convergence` | Convergence metrics | COMPLETE |
| `compare_trials` | Side-by-side comparison | COMPLETE |
| `get_best_design` | Best design details | COMPLETE |
| `generate_report` | Markdown reports | COMPLETE |
| `export_data` | CSV/JSON export | COMPLETE |
| `explain_physics` | FEA concepts | COMPLETE |
| `recommend_method` | Algorithm recommendation | COMPLETE |
| `query_extractors` | Extractor list | COMPLETE |
---
## Phase 1: Canvas with React Flow - COMPLETE
### Core Components
| Component | Location | Status |
|-----------|----------|--------|
| Schema | `frontend/src/lib/canvas/schema.ts` | COMPLETE |
| Intent Serializer | `frontend/src/lib/canvas/intent.ts` | COMPLETE |
| Validation | `frontend/src/lib/canvas/validation.ts` | COMPLETE |
| Templates | `frontend/src/lib/canvas/templates.ts` | COMPLETE |
| Canvas Store | `frontend/src/hooks/useCanvasStore.ts` | COMPLETE |
| Main Canvas | `frontend/src/components/canvas/AtomizerCanvas.tsx` | COMPLETE |
### Node Types (8)
| Node | Icon | Color | Status |
|------|------|-------|--------|
| Model | `Cube` | Blue | COMPLETE |
| Solver | `Cpu` | Violet | COMPLETE |
| Design Variable | `SlidersHorizontal` | Emerald | COMPLETE |
| Extractor | `FlaskConical` | Cyan | COMPLETE |
| Objective | `Target` | Rose | COMPLETE |
| Constraint | `ShieldAlert` | Amber | COMPLETE |
| Algorithm | `BrainCircuit` | Indigo | COMPLETE |
| Surrogate | `Rocket` | Pink | COMPLETE |
### Panels
| Panel | Purpose | Status |
|-------|---------|--------|
| NodeConfigPanel | Configure selected node | COMPLETE |
| ValidationPanel | Display validation errors | COMPLETE |
| ExecuteDialog | Confirm study creation | COMPLETE |
| ChatPanel | Claude chat sidebar | COMPLETE |
| ConfigImporter | Load from study/JSON | COMPLETE |
| TemplateSelector | Choose workflow template | COMPLETE |
---
## Phase 2: LLM Intelligence Layer - COMPLETE
### Canvas MCP Tools
| Tool | Purpose | Status |
|------|---------|--------|
| `validate_canvas_intent` | Validate graph before execution | COMPLETE |
| `execute_canvas_intent` | Create study + optionally run | COMPLETE |
| `interpret_canvas_intent` | Get recommendations | COMPLETE |
### Canvas Chat Hook
| Hook | File | Status |
|------|------|--------|
| `useCanvasChat` | `frontend/src/hooks/useCanvasChat.ts` | COMPLETE |
Features:
- `processWithClaude(intent)` - Full processing with study creation
- `validateWithClaude(intent)` - Validation only
- `analyzeWithClaude(intent)` - Get recommendations
---
## Phase 3: Bidirectional Sync - COMPLETE
| Feature | Status |
|---------|--------|
| Session persistence (SQLite) | COMPLETE |
| Context builder | COMPLETE |
| Canvas to Chat bridge | COMPLETE |
| Study context loading | COMPLETE |
---
## Phase 4: Templates & Polish - COMPLETE
### Templates
| Template | Description | Complexity |
|----------|-------------|------------|
| Mass Minimization | Single-objective mass reduction | Simple |
| Multi-Objective | Mass + displacement Pareto | Medium |
| Turbo Mode | Neural-accelerated | Advanced |
| Mirror WFE | Zernike optimization | Advanced |
| Frequency Target | Modal analysis | Medium |
### UI Features
| Feature | Status |
|---------|--------|
| Lucide icons (no emojis) | COMPLETE |
| Dark theme (Atomaster) | COMPLETE |
| Responsive layout | COMPLETE |
| Full-screen canvas | COMPLETE |
| Floating action buttons | COMPLETE |
---
## Canvas V3 Upgrade - COMPLETE
All Canvas V2 and V3 features have been implemented:
| Feature | Status |
|---------|--------|
| Professional Lucide icons | COMPLETE |
| Responsive full-screen layout | COMPLETE |
| Auto-load from optimization_config.json | COMPLETE |
| NX model introspection endpoint | COMPLETE |
| Expression search dropdown | COMPLETE |
| "Process with Claude" button | COMPLETE |
| MCP canvas tools | COMPLETE |
| Backend study list endpoint | COMPLETE |
| File browser for model selection | COMPLETE |
| Introspection panel (expressions, extractors) | COMPLETE |
| Claude WebSocket fixes | COMPLETE |
| Health check endpoint | COMPLETE |
---
## File Inventory
### MCP Server (`mcp-server/atomizer-tools/`)
```
src/
├── index.ts # Server entry (imports canvasTools)
├── tools/
│ ├── study.ts # Study management
│ ├── optimization.ts # Optimization control
│ ├── analysis.ts # Analysis tools
│ ├── reporting.ts # Report generation
│ ├── physics.ts # Physics explanations
│ ├── canvas.ts # Canvas intent tools
│ └── admin.ts # Power mode tools
└── utils/
└── paths.ts # Path utilities
```
### Backend Services (`atomizer-dashboard/backend/api/services/`)
```
__init__.py
claude_agent.py # Full Claude API integration (722 lines)
claude_cli_agent.py # CLI-based agent (202 lines)
conversation_store.py # SQLite persistence (295 lines)
session_manager.py # Session lifecycle (425 lines)
context_builder.py # Context assembly (246 lines)
nx_introspection.py # NX model introspection (NEW)
```
### Backend Routes (`atomizer-dashboard/backend/api/routes/`)
```
__init__.py
terminal.py # Claude WebSocket endpoint
optimization.py # Optimization API
studies.py # Study configuration
files.py # File browser API (NEW)
nx.py # NX introspection API (NEW)
```
### Frontend Canvas (`atomizer-dashboard/frontend/src/components/canvas/`)
```
AtomizerCanvas.tsx # Main canvas component
nodes/
├── index.ts # Node type registry
├── BaseNode.tsx # Base with multiple handles
├── ModelNode.tsx
├── SolverNode.tsx
├── DesignVarNode.tsx
├── ExtractorNode.tsx
├── ObjectiveNode.tsx
├── ConstraintNode.tsx
├── AlgorithmNode.tsx
└── SurrogateNode.tsx
panels/
├── NodeConfigPanel.tsx # Node configuration sidebar
├── ValidationPanel.tsx # Validation toast display
├── ExecuteDialog.tsx # Execute confirmation modal
├── ChatPanel.tsx # Claude chat sidebar
├── ConfigImporter.tsx # Study import dialog
├── TemplateSelector.tsx # Workflow template chooser
├── FileBrowser.tsx # File picker for model selection (NEW)
├── IntrospectionPanel.tsx # Model introspection results (NEW)
└── ExpressionSelector.tsx # Expression search dropdown (NEW)
palette/
└── NodePalette.tsx
```
### Canvas Library (`atomizer-dashboard/frontend/src/lib/canvas/`)
```
schema.ts # Type definitions
intent.ts # Serialization (174 lines)
validation.ts # Graph validation
templates.ts # Workflow templates
index.ts # Exports
```
---
## Testing Checklist
### Build Verification
```bash
# Build MCP server
cd mcp-server/atomizer-tools
npm run build
# Expected: Compiles without errors
# Build frontend
cd atomizer-dashboard/frontend
npm run build
# Expected: Compiles without errors
```
### Functional Testing
- [ ] Navigate to `/canvas`
- [ ] Drag nodes from palette
- [ ] Connect nodes with edges
- [ ] Configure node properties
- [ ] Click "Validate"
- [ ] Click "Process with Claude"
- [ ] Chat panel responds
- [ ] Import from existing study
- [ ] Select workflow template
- [ ] Expression dropdown works
---
## References
- [Canvas Documentation](CANVAS.md) - Full Canvas Builder guide
- [Dashboard Overview](DASHBOARD.md) - Main dashboard documentation
- [RALPH_LOOP_CANVAS_V2](../plans/RALPH_LOOP_CANVAS_V2.md) - V2 upgrade prompt
---
*Implementation completed via autonomous Claude Code sessions.*