feat: Improve dashboard performance and Claude terminal context

- Add trial limiting (300 max) and reduce polling to 15s for large studies
- Make dashboard layout wider with col-span adjustments
- Claude terminal now runs from Atomizer root for CLAUDE.md/skills access
- Add study context display in terminal on connect
- Add KaTeX math rendering styles for study reports
- Add surrogate tuner module for hyperparameter optimization
- Fix backend proxy to port 8001

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

.claude/settings.local.json

@@ -15,7 +15,39 @@
       "Bash(C:UsersAntoineminiconda3envsatomizerpython.exe run_adaptive_mirror_optimization.py --fea-budget 100 --batch-size 5 --strategy hybrid)",
       "Bash(/c/Users/Antoine/miniconda3/envs/atomizer/python.exe:*)",
       "Bash(npm run build:*)",
-      "Bash(npm uninstall:*)"
+      "Bash(npm uninstall:*)",
+      "Bash(netstat:*)",
+      "Bash(findstr:*)",
+      "Bash(curl:*)",
+      "Bash(npx tsc:*)",
+      "Bash(atomizer-dashboard/README.md )",
+      "Bash(atomizer-dashboard/backend/api/main.py )",
+      "Bash(atomizer-dashboard/backend/api/routes/optimization.py )",
+      "Bash(atomizer-dashboard/backend/api/routes/claude.py )",
+      "Bash(atomizer-dashboard/backend/api/routes/terminal.py )",
+      "Bash(atomizer-dashboard/backend/api/services/ )",
+      "Bash(atomizer-dashboard/backend/requirements.txt )",
+      "Bash(atomizer-dashboard/frontend/package.json )",
+      "Bash(atomizer-dashboard/frontend/package-lock.json )",
+      "Bash(atomizer-dashboard/frontend/src/components/ClaudeChat.tsx )",
+      "Bash(atomizer-dashboard/frontend/src/components/ClaudeTerminal.tsx )",
+      "Bash(atomizer-dashboard/frontend/src/components/dashboard/ControlPanel.tsx )",
+      "Bash(atomizer-dashboard/frontend/src/pages/Dashboard.tsx )",
+      "Bash(atomizer-dashboard/frontend/src/context/ )",
+      "Bash(atomizer-dashboard/frontend/src/pages/Home.tsx )",
+      "Bash(atomizer-dashboard/frontend/src/App.tsx )",
+      "Bash(atomizer-dashboard/frontend/src/api/client.ts )",
+      "Bash(atomizer-dashboard/frontend/src/components/layout/Sidebar.tsx )",
+      "Bash(atomizer-dashboard/frontend/src/index.css )",
+      "Bash(atomizer-dashboard/frontend/src/pages/Results.tsx )",
+      "Bash(atomizer-dashboard/frontend/tailwind.config.js )",
+      "Bash(docs/07_DEVELOPMENT/DASHBOARD_IMPROVEMENT_PLAN.md)",
+      "Bash(taskkill:*)",
+      "Bash(xargs:*)",
+      "Bash(cmd.exe /c:*)",
+      "Bash(powershell.exe -Command:*)",
+      "Bash(where:*)",
+      "Bash(type %USERPROFILE%.claude*)"
     ],
     "deny": [],
     "ask": []

.claude/skills/create-study.md

@@ -1,7 +1,7 @@
 # Create Optimization Study Skill
 
-**Last Updated**: November 26, 2025
-**Version**: 2.0 - Protocol Reference + Code Patterns (Centralized)
+**Last Updated**: December 4, 2025
+**Version**: 2.1 - Added Mandatory Documentation Requirements
 
 You are helping the user create a complete Atomizer optimization study from a natural language description.
 
@@ -9,6 +9,39 @@ You are helping the user create a complete Atomizer optimization study from a na
 
 ---
 
+## MANDATORY DOCUMENTATION CHECKLIST
+
+**EVERY study MUST have these files. A study is NOT complete without them:**
+
+| File | Purpose | When Created |
+|------|---------|--------------|
+| `README.md` | **Engineering Blueprint** - Full mathematical formulation, design variables, objectives, algorithm config | At study creation |
+| `STUDY_REPORT.md` | **Results Tracking** - Progress, best designs, surrogate accuracy, recommendations | At study creation (template) |
+
+**README.md Requirements (11 sections)**:
+1. Engineering Problem (objective, physical system)
+2. Mathematical Formulation (objectives, design variables, constraints with LaTeX)
+3. Optimization Algorithm (config, properties, return format)
+4. Simulation Pipeline (trial execution flow diagram)
+5. Result Extraction Methods (extractor details, code snippets)
+6. Neural Acceleration (surrogate config, expected performance)
+7. Study File Structure (directory tree)
+8. Results Location (output files)
+9. Quick Start (commands)
+10. Configuration Reference (config.json mapping)
+11. References
+
+**STUDY_REPORT.md Requirements**:
+- Executive Summary (trial counts, best values)
+- Optimization Progress (iteration history, convergence)
+- Best Designs Found (FEA-validated)
+- Neural Surrogate Performance (R², MAE)
+- Engineering Recommendations
+
+**FAILURE MODE**: If you create a study without README.md and STUDY_REPORT.md, the user cannot understand what the study does, the dashboard cannot display documentation, and the study is incomplete.
+
+---
+
 ## Protocol Reference (MUST USE)
 
 This section defines ALL available components. When generating `run_optimization.py`, use ONLY these documented patterns.