fix: remove non-empty local copies of remote storage dirs (#2845)

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).

snakemake/dag.py

@@ -420,7 +420,9 @@ async def cleanup_storage_objects(self):
                     for f in chain(job.input, job.output):
                         if f.is_storage and f not in cleaned:
                             f.storage_object.cleanup()
-                            tg.create_task(f.remove(only_local=True))
+                            tg.create_task(
+                                f.remove(remove_non_empty_dir=True, only_local=True)
+                            )
                             cleaned.add(f)
 
     def create_conda_envs(self, dryrun=False, quiet=False):