feat: Add neural loop automation - templates, auto-trainer, CLI

Closes the neural training loop with automated workflow:
- atomizer.py: One-command neural workflow CLI
- auto_trainer.py: Auto-training trigger system (50pt threshold)
- template_loader.py: Study creation from templates
- study_reset.py: Study reset/cleanup utility
- 3 templates: beam stiffness, bracket stress, frequency tuning
- State assessment document (Nov 25)

Usage: python atomizer.py neural-optimize --study my_study --trials 500

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

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

templates/bracket_stress_minimization.json

@@ -0,0 +1,117 @@
+{
+  "study_name": "bracket_stress_minimization",
+  "description": "Bracket Stress Minimization - Minimize peak stress while maintaining stiffness",
+  "engineering_context": "L-bracket or mounting bracket optimization. Minimize stress concentrations by adjusting fillet radii, wall thickness, and material distribution.",
+  "template_info": {
+    "category": "structural",
+    "analysis_type": "static",
+    "typical_applications": ["mounting brackets", "L-brackets", "gusset plates", "corner joints"],
+    "required_nx_expressions": ["wall_thickness", "fillet_radius", "web_thickness"]
+  },
+
+  "optimization_settings": {
+    "protocol": "protocol_10_single_objective",
+    "n_trials": 75,
+    "sampler": "TPE",
+    "pruner": "MedianPruner",
+    "timeout_per_trial": 400
+  },
+
+  "design_variables": [
+    {
+      "parameter": "wall_thickness",
+      "bounds": [2, 10],
+      "description": "Main wall thickness (mm)",
+      "units": "mm"
+    },
+    {
+      "parameter": "fillet_radius",
+      "bounds": [3, 20],
+      "description": "Corner fillet radius (mm) - stress relief",
+      "units": "mm"
+    },
+    {
+      "parameter": "web_thickness",
+      "bounds": [1, 8],
+      "description": "Stiffening web thickness (mm)",
+      "units": "mm"
+    },
+    {
+      "parameter": "rib_count",
+      "bounds": [0, 5],
+      "description": "Number of stiffening ribs",
+      "type": "integer"
+    }
+  ],
+
+  "objectives": [
+    {
+      "name": "max_stress",
+      "goal": "minimize",
+      "weight": 1.0,
+      "description": "Peak von Mises stress (MPa)",
+      "target": 50,
+      "extraction": {
+        "action": "extract_stress",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "stress",
+          "metric": "max_von_mises"
+        }
+      }
+    }
+  ],
+
+  "constraints": [
+    {
+      "name": "max_displacement_limit",
+      "type": "less_than",
+      "threshold": 0.5,
+      "description": "Maximum displacement < 0.5mm for stiffness requirement",
+      "extraction": {
+        "action": "extract_displacement",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "displacement",
+          "metric": "max"
+        }
+      }
+    },
+    {
+      "name": "max_mass_limit",
+      "type": "less_than",
+      "threshold": 200,
+      "description": "Maximum mass < 200g for weight budget",
+      "extraction": {
+        "action": "extract_mass",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "mass",
+          "metric": "total"
+        }
+      }
+    }
+  ],
+
+  "simulation": {
+    "model_file": "Bracket.prt",
+    "sim_file": "Bracket_sim1.sim",
+    "fem_file": "Bracket_fem1.fem",
+    "solver": "nastran",
+    "analysis_types": ["static"]
+  },
+
+  "reporting": {
+    "generate_plots": true,
+    "save_incremental": true,
+    "llm_summary": false
+  },
+
+  "training_data_export": {
+    "enabled": true,
+    "export_dir": "atomizer_field_training_data/${study_name}",
+    "export_every_n_trials": 1,
+    "include_mesh": true,
+    "compress": false
+  }
+}