feat: Add AtomizerField training data export and intelligent model discovery

Major additions:
- Training data export system for AtomizerField neural network training
- Bracket stiffness optimization study with 50+ training samples
- Intelligent NX model discovery (auto-detect solutions, expressions, mesh)
- Result extractors module for displacement, stress, frequency, mass
- User-generated NX journals for advanced workflows
- Archive structure for legacy scripts and test outputs
- Protocol documentation and dashboard launcher

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

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

archive/scripts/reorganize_study.py

@@ -0,0 +1,97 @@
+"""
+Reorganize simple_beam_optimization study to new structure.
+Handles locked files gracefully.
+"""
+import shutil
+from pathlib import Path
+import time
+
+study_dir = Path("studies/simple_beam_optimization")
+
+# Check current state
+print("Current directory structure:")
+print(f"  1_setup exists: {(study_dir / '1_setup').exists()}")
+print(f"  2_substudies exists: {(study_dir / '2_substudies').exists()}")
+print(f"  3_reports exists: {(study_dir / '3_reports').exists()}")
+print()
+
+# Copy full_optimization_50trials if not already done
+src = study_dir / "substudies" / "full_optimization_50trials"
+dst = study_dir / "2_substudies" / "04_full_optimization_50trials"
+
+if src.exists() and not dst.exists():
+    print(f"Copying {src.name} to {dst.name}...")
+    try:
+        shutil.copytree(src, dst)
+        print(f"  SUCCESS: Copied to {dst}")
+    except Exception as e:
+        print(f"  WARNING: {e}")
+        print(f"  Will attempt to continue...")
+
+# Move OPTIMIZATION_RESULTS_50TRIALS.md
+old_results_file = study_dir / "OPTIMIZATION_RESULTS_50TRIALS.md"
+new_results_file = dst / "OPTIMIZATION_RESULTS.md"
+
+if old_results_file.exists() and not new_results_file.exists():
+    print(f"\nMoving {old_results_file.name}...")
+    try:
+        shutil.move(str(old_results_file), str(new_results_file))
+        print(f"  SUCCESS: Moved to {new_results_file}")
+    except Exception as e:
+        print(f"  WARNING: {e}")
+
+# Move COMPREHENSIVE_BENCHMARK_RESULTS.md
+old_bench_file = study_dir / "COMPREHENSIVE_BENCHMARK_RESULTS.md"
+new_bench_file = study_dir / "3_reports" / "COMPREHENSIVE_BENCHMARK_RESULTS.md"
+
+if old_bench_file.exists() and not new_bench_file.exists():
+    print(f"\nMoving {old_bench_file.name}...")
+    try:
+        shutil.move(str(old_bench_file), str(new_bench_file))
+        print(f"  SUCCESS: Moved to {new_bench_file}")
+    except Exception as e:
+        print(f"  WARNING: {e}")
+
+# Try to remove old substudies directory (may fail due to locked files - that's OK)
+old_substudies = study_dir / "substudies"
+if old_substudies.exists():
+    print(f"\nAttempting to remove old 'substudies' directory...")
+    try:
+        # Try multiple times in case files get unlocked
+        for attempt in range(3):
+            try:
+                shutil.rmtree(old_substudies)
+                print(f"  SUCCESS: Removed old 'substudies' directory")
+                break
+            except Exception as e:
+                if attempt < 2:
+                    print(f"  Attempt {attempt + 1} failed, retrying in 1 second...")
+                    time.sleep(1)
+                else:
+                    print(f"  INFO: Could not remove old 'substudies' directory (files may be locked)")
+                    print(f"  You can manually delete it later: {old_substudies}")
+    except Exception as e:
+        print(f"  WARNING: {e}")
+
+# Remove old model directory if empty
+old_model = study_dir / "model"
+if old_model.exists() and not list(old_model.iterdir()):
+    print(f"\nRemoving empty 'model' directory...")
+    try:
+        old_model.rmdir()
+        print(f"  SUCCESS: Removed empty 'model' directory")
+    except Exception as e:
+        print(f"  WARNING: {e}")
+
+print("\n" + "="*70)
+print("Reorganization complete!")
+print("="*70)
+print("\nNew structure:")
+print("  1_setup/ - Pre-optimization setup")
+print("  2_substudies/ - Optimization runs (numbered)")
+print("  3_reports/ - Study-level analysis")
+print()
+print("Next steps:")
+print("  1. Update study_metadata.json")
+print("  2. Create substudy README files")
+print("  3. Delete old 'substudies' folder manually if it still exists")