fix: Smudge non-annexed files, ensuring eol enforcement

Author: effigies

services/datalad/datalad_service/common/git.py

@@ -163,6 +163,9 @@ async def git_commit(
         sentry_sdk.capture_exception(e)
         logger.error(f'Failed to read index after git-annex add: {e}')
         raise OpenNeuroGitError(f'Failed to read index: {e}') from e
+    # Ensure non-annexed files are smudged, e.g., update end-of-lines
+    # but do not "fix" unrelated paths
+    repo.index.add_all(file_paths)
     return await git_commit_index(repo, author, message, parents)