[Feature Request] returning packed object instead of dumping to files

Currently `upgrade_document` has the following signature and always dumps the upgraded step objects into `outpu_dir`.
```python
def upgrade_document(
document: Any, v1_only: bool, v1_1_only: bool, output_dir: str, imports: Set[str]
) -> Any:
```
However, it makes harder to integrate other related tools such as `cwl_utils.parser.load_document` family.
I would be nice if `upgrade_document` has an option that returns a upgraded packed CWL object instead of directly writing upgraded CWL objects.

Start by locating upgrade_document and tracing its callers, especially the handling of output_dir and the cwl_utils.parser.load_document family mentioned in the issue. Review how upgraded step objects are currently packed and written; done means callers can choose a packed upgraded CWL object instead of direct file output while preserving the existing behavior.

Written by the indexing model from the issue text.