diff --git a/.github/workflows/validate_bids-examples.yml b/.github/workflows/validate_bids-examples.yml
index 3d685fbe76..7911ad5c82 100644
--- a/.github/workflows/validate_bids-examples.yml
+++ b/.github/workflows/validate_bids-examples.yml
@@ -103,9 +103,13 @@ jobs:
       working-directory: bids-examples
 
     - name: Show migrated datasets diff
-      run: git diff
+      run: git diff HEAD
       working-directory: bids-examples
 
+    # TODO: commit as a merge from current state of bids-examples
+    # and prior bids-2.0 branch there, but overloading with new updated
+    # state and recording commit hash of bids-specification used.
+
     - name: Validate all BIDS datasets using bids-validator after migration
       run: VALIDATOR_ARGS="--schema file://$PWD/../src/schema.json" bash ./run_tests.sh
       working-directory: bids-examples
diff --git a/tools/schemacode/bidsschematools/migrations.py b/tools/schemacode/bidsschematools/migrations.py
index 684c5d2aa6..1cf0441cf1 100644
--- a/tools/schemacode/bidsschematools/migrations.py
+++ b/tools/schemacode/bidsschematools/migrations.py
@@ -1,7 +1,11 @@
 import json
 import os
 import re
+import subprocess
+from functools import lru_cache
+from itertools import chain
 from pathlib import Path
+from typing import Optional
 
 import bidsschematools as bst
 import bidsschematools.utils
@@ -11,10 +15,14 @@
 TARGET_VERSION = "2.0.0"
 
 
+class NotBIDSDatasetError(Exception):
+    pass
+
+
 def get_bids_version(dataset_path: Path) -> str:
     dataset_description = dataset_path / "dataset_description.json"
     if not dataset_description.exists():
-        raise ValueError(f"dataset_description.json not found in {dataset_path}")
+        raise NotBIDSDatasetError(f"dataset_description.json not found in {dataset_path}")
     return json.loads(dataset_description.read_text())["BIDSVersion"]
 
 
@@ -39,7 +47,7 @@ def migrate_participants(dataset_path: Path):
         old_file = dataset_path / f"participants{ext}"
         new_file = dataset_path / f"subjects{ext}"
         if old_file.exists():
-            os.rename(old_file, new_file)
+            rename_path(old_file, new_file)
             lgr.info(f"   - renamed {old_file} to {new_file}")
             if ext == ".tsv":
                 # Do manual .decode() and .encode() to avoid changing line endings
@@ -53,8 +61,12 @@ def migrate_participants(dataset_path: Path):
 def migrate_dataset(dataset_path):
     lgr.info(f"Migrating dataset at {dataset_path}")
     dataset_path = Path(dataset_path)
-    if get_bids_version(dataset_path) == TARGET_VERSION:
-        lgr.info(f"Dataset already at version {TARGET_VERSION}")
+    try:
+        if get_bids_version(dataset_path) == TARGET_VERSION:
+            lgr.info(f"Dataset already at version {TARGET_VERSION}")
+            return
+    except NotBIDSDatasetError:
+        lgr.warning("%s not a BIDS dataset, skipping", dataset_path)
         return
     # TODO: possibly add a check for BIDS version in dataset_description.json
     # and skip if already 2.0, although ideally transformations
@@ -65,3 +77,32 @@ def migrate_dataset(dataset_path):
     ]:
         lgr.info(f" - applying migration {migration.__name__}")
         migration(dataset_path)
+
+
+@lru_cache
+def path_has_git(path: Path) -> bool:
+    return (path / ".git").exists()
+
+
+def git_topdir(path: Path) -> Optional[Path]:
+    """Return top-level directory of a git repository containing path,
+    or None if not under git."""
+    path = path.absolute()
+    for p in chain([path] if path.is_dir() else [], path.parents):
+        if path_has_git(p):
+            return p
+    return None
+
+
+def rename_path(old_path: Path, new_path: Path):
+    """git aware rename. If under git, use git mv, otherwise just os.rename."""
+    # if under git, use git mv but ensure that on border
+    # crossing (should just use DataLad and `mv` and it would do the right thing!)
+    if (old_git_top := git_topdir(old_path)) != (new_git_top := git_topdir(new_path)):
+        raise NotImplementedError(
+            f"Did not implement moving across git repo boundaries {old_git_top} -> {new_git_top}"
+        )
+    if old_git_top:
+        subprocess.run(["git", "mv", str(old_path), str(new_path)], check=True, cwd=old_git_top)
+    else:
+        os.rename(old_path, new_path)