docs: Update documentation for AtomizerSpec v2.0 unified configuration

Phase 4 documentation updates:
- CANVAS.md: Add AtomizerSpec v2.0 schema, custom extractors section,
  spec REST API endpoints, and updated file structure
- DASHBOARD.md: Add V3.1 release notes, AtomizerSpec API endpoints,
  and unified configuration features
- CLAUDE.md: Add complete AtomizerSpec v2.0 section with code examples,
  MCP tools reference, API endpoints, and updated directory structure

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

docs/04_USER_GUIDES/DASHBOARD.md

@@ -1,7 +1,7 @@
 # Atomizer Dashboard
 
-**Last Updated**: January 16, 2026
-**Version**: 3.0
+**Last Updated**: January 17, 2026
+**Version**: 3.1 (AtomizerSpec v2.0)
 
 ---
 
@@ -9,17 +9,19 @@
 
 The Atomizer Dashboard is a real-time web-based interface for monitoring and analyzing multi-objective optimization studies. Built with React, TypeScript, and Tailwind CSS, it provides comprehensive visualization and interaction capabilities for NSGA-II based structural optimization.
 
+**New in V3.1**: All studies now use **AtomizerSpec v2.0** as the unified configuration format. The `atomizer_spec.json` file serves as the single source of truth for Canvas, Backend, Claude, and the Optimization Engine.
+
 ### Major Features
 
 | Feature | Route | Description |
 |---------|-------|-------------|
-| **Canvas Builder** | `/canvas` | Visual node-based workflow designer |
+| **Canvas Builder** | `/canvas` | Visual node-based workflow designer (AtomizerSpec v2.0) |
 | **Live Dashboard** | `/dashboard` | Real-time optimization monitoring |
 | **Results Viewer** | `/results` | Markdown reports with charts |
 | **Analytics** | `/analytics` | Cross-study comparison |
-| **Claude Chat** | Global | AI-powered study creation |
+| **Claude Chat** | Global | AI-powered study creation with spec tools |
 
-> **New in V2**: The [Canvas Builder](CANVAS.md) provides a visual, drag-and-drop interface for designing optimization workflows with Claude AI integration.
+> **New in V3.1**: The [Canvas Builder](CANVAS.md) now uses AtomizerSpec v2.0 as the unified configuration format, with support for custom extractors and real-time WebSocket synchronization.
 
 ---
 
@@ -237,6 +239,43 @@ Reusable markdown rendering component:
 
 ## API Endpoints
 
+### AtomizerSpec (V3.1)
+
+#### GET `/api/studies/{study_id}/spec`
+Get the full AtomizerSpec for a study.
+
+**Response**:
+```json
+{
+  "meta": { "version": "2.0", "study_name": "..." },
+  "model": { "sim": { "path": "...", "solver": "nastran" } },
+  "design_variables": [...],
+  "extractors": [...],
+  "objectives": [...],
+  "constraints": [...],
+  "optimization": { "algorithm": { "type": "TPE" }, "budget": { "max_trials": 100 } },
+  "canvas": { "edges": [...], "layout_version": "2.0" }
+}
+```
+
+#### PUT `/api/studies/{study_id}/spec`
+Replace the entire spec with validation.
+
+#### PATCH `/api/studies/{study_id}/spec`
+Partial update using JSONPath. Body: `{ "path": "design_variables[0].bounds.max", "value": 15.0 }`
+
+#### POST `/api/studies/{study_id}/spec/validate`
+Validate spec and return detailed report. Returns: `{ "valid": true, "errors": [], "warnings": [] }`
+
+#### POST `/api/studies/{study_id}/spec/nodes`
+Add a new node (design variable, extractor, objective, constraint).
+
+#### PATCH `/api/studies/{study_id}/spec/nodes/{node_id}`
+Update an existing node's properties.
+
+#### DELETE `/api/studies/{study_id}/spec/nodes/{node_id}`
+Remove a node and clean up related edges.
+
 ### Studies
 
 #### GET `/api/optimization/studies`
@@ -576,6 +615,31 @@ if (!objectives || !designVariables) return <EmptyState />;
 
 ## Recent Updates
 
+### January 2026 (V3.1) - AtomizerSpec v2.0
+
+- [x] **AtomizerSpec v2.0**: Unified configuration architecture
+  - **Single Source of Truth**: One `atomizer_spec.json` file for Canvas, Backend, Claude, and Optimization Engine
+  - **Spec REST API**: Full CRUD operations at `/api/studies/{id}/spec`
+  - **Pydantic Validation**: Backend validation with detailed error messages
+  - **Legacy Migration**: Automatic migration from `optimization_config.json`
+  - **29 Studies Migrated**: All existing studies converted to v2.0 format
+
+- [x] **Custom Extractors**: Define custom Python extraction functions in the spec
+  - **Security Validation**: Code checked for dangerous patterns
+  - **Runtime Loading**: Functions executed during optimization
+  - **Canvas UI**: Code editor panel for custom extractor nodes
+
+- [x] **WebSocket Sync**: Real-time spec synchronization
+  - Multiple clients stay synchronized
+  - Optimistic updates with rollback on error
+  - Conflict detection with hash comparison
+
+- [x] **Comprehensive Testing**: Full test coverage for Phase 4
+  - Unit tests for SpecManager and Pydantic models
+  - API integration tests for all spec endpoints
+  - Migration tests for legacy config formats
+  - E2E tests for complete workflow
+
 ### January 2026 (V3.0)
 
 - [x] **Canvas Builder V3**: Major upgrade with model introspection and Claude fixes