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/beam_stiffness_optimization.json

@@ -0,0 +1,112 @@
+{
+  "study_name": "beam_stiffness_optimization",
+  "description": "Beam Stiffness Optimization - Maximize stiffness while minimizing mass",
+  "engineering_context": "Cantilever beam optimization. Find optimal cross-section dimensions to maximize bending stiffness under tip load while minimizing weight.",
+  "template_info": {
+    "category": "structural",
+    "analysis_type": "static",
+    "typical_applications": ["cantilever beams", "support arms", "brackets"],
+    "required_nx_expressions": ["beam_width", "beam_height", "beam_length"]
+  },
+
+  "optimization_settings": {
+    "protocol": "protocol_10_single_objective",
+    "n_trials": 50,
+    "sampler": "TPE",
+    "pruner": "MedianPruner",
+    "timeout_per_trial": 300
+  },
+
+  "design_variables": [
+    {
+      "parameter": "beam_width",
+      "bounds": [10, 50],
+      "description": "Beam cross-section width (mm)",
+      "units": "mm"
+    },
+    {
+      "parameter": "beam_height",
+      "bounds": [10, 80],
+      "description": "Beam cross-section height (mm)",
+      "units": "mm"
+    },
+    {
+      "parameter": "beam_length",
+      "bounds": [100, 500],
+      "description": "Beam length (mm)",
+      "units": "mm"
+    }
+  ],
+
+  "objectives": [
+    {
+      "name": "stiffness",
+      "goal": "maximize",
+      "weight": 1.0,
+      "description": "Effective bending stiffness (inverse of tip displacement under unit load)",
+      "target": 10000,
+      "extraction": {
+        "action": "extract_displacement",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "displacement",
+          "metric": "max",
+          "invert": true
+        }
+      }
+    }
+  ],
+
+  "constraints": [
+    {
+      "name": "max_mass_limit",
+      "type": "less_than",
+      "threshold": 500,
+      "description": "Maximum mass < 500g",
+      "extraction": {
+        "action": "extract_mass",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "mass",
+          "metric": "total"
+        }
+      }
+    },
+    {
+      "name": "max_stress_limit",
+      "type": "less_than",
+      "threshold": 200,
+      "description": "Maximum von Mises stress < 200 MPa",
+      "extraction": {
+        "action": "extract_stress",
+        "domain": "result_extraction",
+        "params": {
+          "result_type": "stress",
+          "metric": "max_von_mises"
+        }
+      }
+    }
+  ],
+
+  "simulation": {
+    "model_file": "Beam.prt",
+    "sim_file": "Beam_sim1.sim",
+    "fem_file": "Beam_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
+  }
+}