feat: Pre-migration checkpoint - updated docs and utilities

Updates before optimization_engine migration:
- Updated migration plan to v2.1 with complete file inventory
- Added OP_07 disk optimization protocol
- Added SYS_16 self-aware turbo protocol
- Added study archiver and cleanup utilities
- Added ensemble surrogate module
- Updated NX solver and session manager
- Updated zernike HTML generator
- Added context engineering plan
- LAC session insights updates

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

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

run_cleanup.py

@@ -0,0 +1,67 @@
+"""Run cleanup excluding protected studies."""
+import sys
+from pathlib import Path
+
+# Add project root to path
+sys.path.insert(0, str(Path(__file__).parent))
+
+from optimization_engine.utils.study_cleanup import cleanup_study, get_study_info
+
+m1_dir = Path(r"C:\Users\antoi\Atomizer\studies\M1_Mirror")
+
+# Studies to SKIP (user requested)
+skip_patterns = [
+    "cost_reduction_V10",
+    "cost_reduction_V11",
+    "cost_reduction_V12",
+    "flat_back",
+]
+
+# Parse args
+dry_run = "--execute" not in sys.argv
+keep_best = 5
+
+total_saved = 0
+studies_to_clean = []
+
+print("=" * 75)
+print(f"CLEANUP (excluding V10-V12 and flat_back studies)")
+print(f"Mode: {'DRY RUN' if dry_run else 'EXECUTE'}")
+print("=" * 75)
+print(f"{'Study':<45} {'Trials':>7} {'Size':>8} {'Savings':>8}")
+print("-" * 75)
+
+for study_path in sorted(m1_dir.iterdir()):
+    if not study_path.is_dir():
+        continue
+    # Check if has iterations
+    if not (study_path / "2_iterations").exists():
+        continue
+
+    # Skip protected studies
+    skip = False
+    for pattern in skip_patterns:
+        if pattern in study_path.name:
+            skip = True
+            break
+
+    if skip:
+        info = get_study_info(study_path)
+        print(f"{study_path.name:<45} {info['trial_count']:>7}   SKIPPED")
+        continue
+
+    # This study will be cleaned
+    result = cleanup_study(study_path, dry_run=dry_run, keep_best=keep_best)
+    saved = result["space_saved_gb"]
+    total_saved += saved
+    status = "would save" if dry_run else "saved"
+    print(f"{study_path.name:<45} {result['trial_count']:>7} {result['total_size_before']/(1024**3):>7.1f}G {saved:>7.1f}G")
+    studies_to_clean.append(study_path.name)
+
+print("-" * 75)
+print(f"{'TOTAL SAVINGS:':<45} {' '*15} {total_saved:>7.1f}G")
+
+if dry_run:
+    print(f"\n[!] This was a dry run. Run with --execute to actually delete files.")
+else:
+    print(f"\n[OK] Cleanup complete! Freed {total_saved:.1f} GB")