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

- 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

docs/archive/plans/dashboard_enhancement_plan.md

@@ -0,0 +1,95 @@
+# Advanced Dashboard Enhancement Plan
+
+## Objective
+Elevate the Atomizer Dashboard to a "Gemini 3.0 level" experience, focusing on scientific rigor, advanced visualization, and deep integration with the optimization engine. This plan addresses the user's request for a "WAY better" implementation based on the initial master prompt.
+
+## 1. Advanced Visualization Suite (Phase 3 Enhancements)
+**Goal**: Replace basic charts with state-of-the-art scientific visualizations.
+
+### 1.1 Parallel Coordinates Plot
+- **Library**: Recharts (custom implementation) or D3.js wrapped in React.
+- **Features**:
+  - Visualize high-dimensional relationships between design variables and objectives.
+  - Interactive brushing/filtering to isolate high-performing designs.
+  - Color coding by objective value (e.g., mass or stress).
+
+### 1.2 Hypervolume Evolution
+- **Goal**: Track the progress of multi-objective optimization.
+- **Implementation**:
+  - Calculate hypervolume metric for each generation/batch.
+  - Plot evolution over time to show convergence speed and quality.
+
+### 1.3 Pareto Front Evolution
+- **Goal**: Visualize the trade-off surface between conflicting objectives.
+- **Implementation**:
+  - 2D/3D scatter plot of objectives.
+  - Animation slider to show how the front evolves over trials.
+  - Highlight the "current best" non-dominated solutions.
+
+### 1.4 Parameter Correlation Matrix
+- **Goal**: Identify relationships between variables.
+- **Implementation**:
+  - Heatmap showing Pearson/Spearman correlation coefficients.
+  - Helps users understand which variables drive performance.
+
+## 2. Iteration Analysis & 3D Viewer (Phase 4)
+**Goal**: Deep dive into individual trial results with 3D context.
+
+### 2.1 Advanced Trial Table
+- **Features**:
+  - Sortable, filterable columns for all variables and objectives.
+  - "Compare" mode: Select 2-3 trials to view side-by-side.
+  - Status indicators with detailed tooltips (e.g., pruning reasons).
+
+### 2.2 3D Mesh Viewer (Three.js)
+- **Integration**:
+  - Load `.obj` or `.gltf` files converted from Nastran `.bdf` or `.op2`.
+  - **Color Mapping**: Overlay stress/displacement results on the mesh.
+  - **Controls**: Orbit, zoom, pan, section cuts.
+  - **Comparison**: Split-screen view for comparing baseline vs. optimized geometry.
+
+## 3. Report Generation (Phase 5)
+**Goal**: Automated, publication-ready reporting.
+
+### 3.1 Dynamic Report Builder
+- **Features**:
+  - Markdown-based editor with live preview.
+  - Drag-and-drop charts from the dashboard into the report.
+  - LLM integration: "Explain this convergence plot" -> Generates text.
+
+### 3.2 Export Options
+- **Formats**: PDF (via `react-to-print` or server-side generation), HTML, Markdown.
+- **Content**: Includes high-res charts, tables, and 3D snapshots.
+
+## 4. UI/UX Polish (Scientific Theme)
+**Goal**: Professional, "Dark Mode" scientific aesthetic.
+
+- **Typography**: Use a monospaced font for data (e.g., JetBrains Mono, Fira Code) and a clean sans-serif for UI (Inter).
+- **Color Palette**:
+  - Background: `#0a0a0a` (Deep black/gray).
+  - Accents: Neon cyan/blue for data, muted gray for UI.
+  - Status: Traffic light colors (Green/Yellow/Red) but desaturated/neon.
+- **Layout**:
+  - Collapsible sidebars for maximum data visibility.
+  - "Zen Mode" for focusing on specific visualizations.
+  - Dense data display (compact rows, small fonts) for information density.
+
+## Implementation Roadmap
+
+1.  **Step 1: Advanced Visualizations**
+    - Implement Parallel Coordinates.
+    - Implement Pareto Front Plot.
+    - Enhance Convergence Plot with confidence intervals (if available).
+
+2.  **Step 2: Iteration Analysis**
+    - Build the advanced data table with sorting/filtering.
+    - Create the "Compare Trials" view.
+
+3.  **Step 3: 3D Viewer Foundation**
+    - Set up Three.js canvas.
+    - Implement basic mesh loading (placeholder geometry first).
+    - Add color mapping logic.
+
+4.  **Step 4: Reporting & Polish**
+    - Build the report editor.
+    - Apply the strict "Scientific Dark" theme globally.