feat: Add dashboard chat integration and MCP server

Major changes:
- Dashboard: WebSocket-based chat with session management
- Dashboard: New chat components (ChatPane, ChatInput, ModeToggle)
- Dashboard: Enhanced UI with parallel coordinates chart
- MCP Server: New atomizer-tools server for Claude integration
- Extractors: Enhanced Zernike OPD extractor
- Reports: Improved report generator

New studies (configs and scripts only):
- M1 Mirror: Cost reduction campaign studies
- Simple Beam, Simple Bracket, UAV Arm studies

Note: Large iteration data (2_iterations/, best_design_archive/)
excluded via .gitignore - kept on local Gitea only.

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

studies/Simple_Bracket/bracket_pareto_3obj/1_setup/optimization_config.json

@@ -0,0 +1,146 @@
+{
+  "study_name": "bracket_pareto_3obj",
+  "description": "Three-objective Pareto optimization: minimize mass, minimize stress, maximize stiffness",
+  "engineering_context": "Generated by StudyWizard on 2025-12-06 14:43",
+  "template_info": {
+    "category": "structural",
+    "analysis_type": "static",
+    "typical_applications": [],
+    "neural_enabled": false
+  },
+  "optimization_settings": {
+    "protocol": "protocol_11_multi",
+    "n_trials": 100,
+    "sampler": "NSGAIISampler",
+    "pruner": null,
+    "timeout_per_trial": 400
+  },
+  "design_variables": [
+    {
+      "parameter": "support_angle",
+      "bounds": [
+        20,
+        70
+      ],
+      "description": "Angle of support arm relative to base",
+      "units": "degrees"
+    },
+    {
+      "parameter": "tip_thickness",
+      "bounds": [
+        30,
+        60
+      ],
+      "description": "Thickness at bracket tip where load is applied",
+      "units": "mm"
+    }
+  ],
+  "objectives": [
+    {
+      "name": "mass",
+      "goal": "minimize",
+      "weight": 1.0,
+      "description": "Total bracket mass (kg)",
+      "extraction": {
+        "action": "extract_mass_from_bdf",
+        "domain": "result_extraction",
+        "params": {}
+      }
+    },
+    {
+      "name": "stress",
+      "goal": "minimize",
+      "weight": 1.0,
+      "description": "Maximum von Mises stress (MPa)",
+      "extraction": {
+        "action": "extract_solid_stress",
+        "domain": "result_extraction",
+        "params": {
+          "metric": "max_von_mises"
+        }
+      }
+    },
+    {
+      "name": "stiffness",
+      "goal": "maximize",
+      "weight": 1.0,
+      "description": "Structural stiffness = Force/Displacement (N/mm)",
+      "extraction": {
+        "action": "extract_displacement",
+        "domain": "result_extraction",
+        "params": {
+          "invert_for_stiffness": true
+        }
+      }
+    }
+  ],
+  "constraints": [
+    {
+      "name": "stress_limit",
+      "type": "less_than",
+      "threshold": 300,
+      "description": "Keep stress below 300 MPa for safety margin",
+      "extraction": {
+        "action": "extract_solid_stress",
+        "domain": "result_extraction",
+        "params": {}
+      }
+    }
+  ],
+  "simulation": {
+    "model_file": "Bracket.prt",
+    "sim_file": "Bracket_sim1.sim",
+    "fem_file": "Bracket_fem1.fem",
+    "solver": "nastran",
+    "analysis_types": [
+      "static"
+    ],
+    "solution_name": "Solution 1",
+    "dat_file": "bracket_sim1-solution_1.dat",
+    "op2_file": "bracket_sim1-solution_1.op2"
+  },
+  "result_extraction": {
+    "mass": {
+      "method": "extract_mass_from_bdf",
+      "extractor_module": "optimization_engine.extractors.bdf_mass_extractor",
+      "function": "extract_mass_from_bdf",
+      "output_unit": "kg"
+    },
+    "stress": {
+      "method": "extract_solid_stress",
+      "extractor_module": "optimization_engine.extractors.extract_von_mises_stress",
+      "function": "extract_solid_stress",
+      "output_unit": "MPa"
+    },
+    "stiffness": {
+      "method": "extract_displacement",
+      "extractor_module": "optimization_engine.extractors.extract_displacement",
+      "function": "extract_displacement",
+      "output_unit": "mm"
+    },
+    "stress_limit": {
+      "method": "extract_solid_stress",
+      "extractor_module": "optimization_engine.extractors.extract_von_mises_stress",
+      "function": "extract_solid_stress",
+      "output_unit": "MPa"
+    }
+  },
+  "reporting": {
+    "generate_plots": true,
+    "save_incremental": true,
+    "llm_summary": true,
+    "generate_pareto_front": true
+  },
+  "neural_acceleration": {
+    "enabled": true,
+    "min_training_points": 50,
+    "auto_train": true,
+    "epochs": 300,
+    "validation_split": 0.2,
+    "nn_trials": 1000,
+    "validate_top_n": 10,
+    "model_file": "surrogate_best.pt",
+    "separate_nn_database": true,
+    "description": "NN results stored in nn_study.db to avoid overloading dashboard"
+  }
+}

studies/Simple_Bracket/bracket_pareto_3obj/1_setup/workflow_config.json

@@ -0,0 +1,5 @@
+{
+  "workflow_id": "bracket_pareto_3obj_workflow",
+  "description": "Workflow for bracket_pareto_3obj",
+  "steps": []
+}