feat: Major update - Physics docs, Zernike OPD, insights, NX journals, tools

Documentation:
- Add docs/06_PHYSICS/ with Zernike fundamentals and OPD method docs
- Add docs/guides/CMA-ES_EXPLAINED.md optimization guide
- Update CLAUDE.md and ATOMIZER_CONTEXT.md with current architecture
- Update OP_01_CREATE_STUDY protocol

Planning:
- Add DYNAMIC_RESPONSE plans for random vibration/PSD support
- Add OPTIMIZATION_ENGINE_MIGRATION_PLAN for code reorganization

Insights System:
- Update design_space, modal_analysis, stress_field, thermal_field insights
- Improve error handling and data validation

NX Journals:
- Add analyze_wfe_zernike.py for Zernike WFE analysis
- Add capture_study_images.py for automated screenshots
- Add extract_expressions.py and introspect_part.py utilities
- Add user_generated_journals/journal_top_view_image_taking.py

Tests & Tools:
- Add comprehensive Zernike OPD test suite
- Add audit_v10 tests for WFE validation
- Add tools for Pareto graphs and mirror data extraction
- Add migrate_studies_to_topics.py utility

Knowledge Base:
- Initialize LAC (Learning Atomizer Core) with failure/success patterns

Dashboard:
- Update Setup.tsx and launch_dashboard.py
- Add restart-dev.bat helper script

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

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

tools/migrate_studies_to_topics.py

@@ -0,0 +1,155 @@
+#!/usr/bin/env python
+"""
+Migration script to reorganize studies into topic-based subfolders.
+
+Run with --dry-run first to preview changes:
+    python migrate_studies_to_topics.py --dry-run
+
+Then run without flag to execute:
+    python migrate_studies_to_topics.py
+"""
+
+import shutil
+import argparse
+from pathlib import Path
+
+STUDIES_DIR = Path(__file__).parent / "studies"
+
+# Topic classification based on study name prefixes
+TOPIC_MAPPING = {
+    'bracket_': 'Simple_Bracket',
+    'drone_gimbal_': 'Drone_Gimbal',
+    'm1_mirror_': 'M1_Mirror',
+    'uav_arm_': 'UAV_Arm',
+    'simple_beam_': 'Simple_Beam',
+}
+
+# Files/folders to skip (not studies)
+SKIP_ITEMS = {
+    'm1_mirror_all_trials_export.csv',  # Data export file
+    '.gitkeep',
+    '__pycache__',
+}
+
+
+def classify_study(study_name: str) -> str:
+    """Determine which topic folder a study belongs to."""
+    for prefix, topic in TOPIC_MAPPING.items():
+        if study_name.startswith(prefix):
+            return topic
+    return '_Other'
+
+
+def get_studies_to_migrate():
+    """Get list of studies that need migration (not already in topic folders)."""
+    studies = []
+
+    for item in STUDIES_DIR.iterdir():
+        # Skip non-directories and special items
+        if not item.is_dir():
+            continue
+        if item.name in SKIP_ITEMS:
+            continue
+        if item.name.startswith('.'):
+            continue
+
+        # Check if this is already a topic folder (contains study subdirs)
+        # A topic folder would have subdirs with 1_setup folders
+        is_topic_folder = any(
+            (sub / "1_setup").exists()
+            for sub in item.iterdir()
+            if sub.is_dir()
+        )
+
+        if is_topic_folder:
+            print(f"[SKIP] {item.name} - already a topic folder")
+            continue
+
+        # Check if this is a study (has 1_setup or optimization_config.json)
+        is_study = (
+            (item / "1_setup").exists() or
+            (item / "optimization_config.json").exists()
+        )
+
+        if is_study:
+            topic = classify_study(item.name)
+            studies.append({
+                'name': item.name,
+                'source': item,
+                'topic': topic,
+                'target': STUDIES_DIR / topic / item.name
+            })
+        else:
+            print(f"[SKIP] {item.name} - not a study (no 1_setup folder)")
+
+    return studies
+
+
+def migrate_studies(dry_run: bool = True):
+    """Migrate studies to topic folders."""
+    studies = get_studies_to_migrate()
+
+    if not studies:
+        print("\nNo studies to migrate. All studies are already organized.")
+        return
+
+    # Group by topic for display
+    by_topic = {}
+    for s in studies:
+        if s['topic'] not in by_topic:
+            by_topic[s['topic']] = []
+        by_topic[s['topic']].append(s)
+
+    print("\n" + "="*60)
+    print("MIGRATION PLAN")
+    print("="*60)
+
+    for topic in sorted(by_topic.keys()):
+        print(f"\n{topic}/")
+        for s in by_topic[topic]:
+            print(f"  +-- {s['name']}/")
+
+    print(f"\nTotal: {len(studies)} studies to migrate")
+
+    if dry_run:
+        print("\n[DRY RUN] No changes made. Run without --dry-run to execute.")
+        return
+
+    # Execute migration
+    print("\n" + "="*60)
+    print("EXECUTING MIGRATION")
+    print("="*60)
+
+    # Create topic folders
+    created_topics = set()
+    for s in studies:
+        topic_dir = STUDIES_DIR / s['topic']
+        if s['topic'] not in created_topics:
+            topic_dir.mkdir(exist_ok=True)
+            created_topics.add(s['topic'])
+            print(f"[CREATE] {s['topic']}/")
+
+    # Move studies
+    for s in studies:
+        try:
+            shutil.move(str(s['source']), str(s['target']))
+            print(f"[MOVE] {s['name']} -> {s['topic']}/{s['name']}")
+        except Exception as e:
+            print(f"[ERROR] Failed to move {s['name']}: {e}")
+
+    print("\n" + "="*60)
+    print("MIGRATION COMPLETE")
+    print("="*60)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Migrate studies to topic folders")
+    parser.add_argument('--dry-run', action='store_true',
+                        help='Preview changes without executing')
+    args = parser.parse_args()
+
+    migrate_studies(dry_run=args.dry_run)
+
+
+if __name__ == "__main__":
+    main()