Add --copy mode to migrate_geant_steps.py

Lets the migration run while another process still has the original files
open for reading: --copy uses shutil.copy2 instead of move, and skips the
now-empty-directory cleanup since the legacy train/ etc. dirs stay populated
by design.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

scripts/migrate_geant_steps.py

@@ -13,7 +13,9 @@ up pool membership from POOL_ASSIGNMENT — decoupling "where it sits today" fro
 "which pool it belongs to".
 
 Defaults to a dry run (prints the planned moves and manifest contents). Pass
---execute to actually move files and write manifests.
+--execute to actually move files and write manifests. Pass --copy as well to
+copy instead of move, leaving the original files in place — e.g. if another
+process is still reading them from their current location.
 """
 
 import argparse
@@ -192,6 +194,13 @@ def main() -> None:
         action="store_true",
         help="Actually move files and write manifests (default: dry run / print plan only)",
     )
+    parser.add_argument(
+        "--copy",
+        action="store_true",
+        help="Copy instead of move, leaving the originals in place "
+        "(e.g. if another process is still reading them). Implies the legacy "
+        "train/ etc. directories are left as-is too, since they won't be empty.",
+    )
     args = parser.parse_args()
 
     src_root = Path(args.root)
@@ -201,9 +210,10 @@ def main() -> None:
     moves, unrecognized = plan_moves(src_root)
     manifests = plan_manifests(src_root)
 
-    print(f"=== {'EXECUTING' if args.execute else 'DRY RUN'}: {src_root} ===\n")
+    verb = "COPY" if args.copy else "MOVE"
+    print(f"=== {'EXECUTING' if args.execute else 'DRY RUN'} ({verb}): {src_root} ===\n")
 
-    print(f"-- {len(moves)} file move(s) --")
+    print(f"-- {len(moves)} file {'copy' if args.copy else 'move'}(s) --")
     for src, dst in moves:
         print(f"  {src.relative_to(src_root)}  ->  {dst.relative_to(src_root)}")
 
@@ -222,11 +232,12 @@ def main() -> None:
         print("\nDry run only — pass --execute to apply.")
         return
 
+    transfer = shutil.copy2 if args.copy else shutil.move
     for src, dst in moves:
         if dst.exists():
             raise FileExistsError(f"refusing to overwrite existing file: {dst}")
         dst.parent.mkdir(parents=True, exist_ok=True)
-        shutil.move(str(src), str(dst))
+        transfer(str(src), str(dst))
 
     for manifest_path, lines in manifests.items():
         manifest_path.parent.mkdir(parents=True, exist_ok=True)
@@ -244,12 +255,14 @@ def main() -> None:
 
     # Legacy pool dirs (train/, sampling_train/, sampling_train/small/) are now
     # empty since their contents were classified by filename, not location —
-    # remove them, but only if a move actually emptied them.
-    for stale_dir in ("train", "sampling_train/small", "sampling_train"):
-        d = src_root / stale_dir
-        if d.is_dir() and not any(d.iterdir()):
-            d.rmdir()
-            print(f"removed now-empty directory: {d.relative_to(src_root)}")
+    # remove them, but only if a move actually emptied them. In --copy mode the
+    # originals are still there by design, so leave these alone entirely.
+    if not args.copy:
+        for stale_dir in ("train", "sampling_train/small", "sampling_train"):
+            d = src_root / stale_dir
+            if d.is_dir() and not any(d.iterdir()):
+                d.rmdir()
+                print(f"removed now-empty directory: {d.relative_to(src_root)}")
 
     print("\nDone.")