diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py
index 383aaae24982..b9e2f927040e 100644
--- a/lib/galaxy/jobs/runners/__init__.py
+++ b/lib/galaxy/jobs/runners/__init__.py
@@ -588,7 +588,7 @@ def _get_metadata_container(
             job_info = JobInfo(
                 working_directory=working_directory or job_wrapper.working_directory,
                 tool_directory=None,
-                job_directory=None,
+                job_directory=job_wrapper.working_directory,
                 tmp_directory=None,
                 home_directory=None,
                 job_directory_type=job_directory_type,
diff --git a/lib/galaxy/objectstore/__init__.py b/lib/galaxy/objectstore/__init__.py
index ca494337ab3e..802b340ed7fc 100644
--- a/lib/galaxy/objectstore/__init__.py
+++ b/lib/galaxy/objectstore/__init__.py
@@ -1627,7 +1627,7 @@ def persist_extra_files(
                 )
 
 
-def get_disk_paths(objectstore: BaseObjectStore) -> Set[str]:
+def get_disk_paths(objectstore: BaseObjectStore, include_extra_dirs=False) -> Set[str]:
     backends = objectstore.get_concrete_store_backends()
     paths = set()
     for backend in backends:
@@ -1636,7 +1636,7 @@ def get_disk_paths(objectstore: BaseObjectStore) -> Set[str]:
             paths.add(disk_path.file_path)
         if disk_path.object_store_cache_path:
             paths.add(disk_path.object_store_cache_path)
-        if disk_path.extra_dirs:
+        if include_extra_dirs and disk_path.extra_dirs:
             for extra_dir in disk_path.extra_dirs.values():
                 paths.add(extra_dir)
     return paths