CWLProv: cannot reproduce workflow runs with Directory input

**cwltool version: 3.1.20220628170238**

Ran [this workflow](https://github.com/RenskeW/cwlprov-provenance/tree/f5dd87a950eeaf7f96bd39dc218164832ff3cbea/prov_data_annotations/example2) by @RenskeW with:

```console
$ cwltool --provenance ro wf.cwl wf_job.yml
```

Then I tried reproducing the run and I got this error:

```console
$ cd ro/workflow/
$ cwltool --debug packed.cwl primary-job.json
INFO /home/simleo/git/workflow-run-crate/tools/cwlprov_to_crate/venv/bin/cwltool 3.1.20220628170238
INFO Resolved 'packed.cwl' to 'file:///home/simleo/repos/cwlprov-provenance/prov_data_annotations/example2/ro/workflow/packed.cwl'
ERROR Input object failed validation:
Anonymous directory object must have 'listing' and 'basename' fields.
Traceback (most recent call last):
File "/home/simleo/git/workflow-run-crate/tools/cwlprov_to_crate/venv/lib/python3.8/site-packages/cwltool/main.py", line 1307, in main
initialized_job_order_object = init_job_order(
File "/home/simleo/git/workflow-run-crate/tools/cwlprov_to_crate/venv/lib/python3.8/site-packages/cwltool/main.py", line 507, in init_job_order
normalizeFilesDirs(job_order_object)
File "/home/simleo/git/workflow-run-crate/tools/cwlprov_to_crate/venv/lib/python3.8/site-packages/cwltool/utils.py", line 474, in normalizeFilesDirs
visit_class(job, ("File", "Directory"), addLocation)
File "/home/simleo/git/workflow-run-crate/tools/cwlprov_to_crate/venv/lib/python3.8/site-packages/cwltool/utils.py", line 216, in visit_class
visit_class(rec[d], cls, op)
File "/home/simleo/git/workflow-run-crate/tools/cwlprov_to_crate/venv/lib/python3.8/site-packages/cwltool/utils.py", line 214, in visit_class
op(rec)
File "/home/simleo/git/workflow-run-crate/tools/cwlprov_to_crate/venv/lib/python3.8/site-packages/cwltool/utils.py", line 434, in addLocation
raise ValidationException(
schema_salad.exceptions.ValidationException: Anonymous directory object must have 'listing' and 'basename' fields.
```

I also had problems with [this other workflow](https://github.com/ResearchObject/workflow-run-crate/tree/a3361b4b4a4939ffeb3ecd85d64bc63ed0be0337/tools/cwlprov_to_crate/grepucase). For each file in the input directory, it does a grep for the given pattern, converts the result to upper case and writes the final result to a file in the output directory.

```console
$ cwltool --provenance ro grepucase.cwl grepucase-job.yml
$ head grepucase_in/*
==> grepucase_in/bar <==
the fat
brown bear
jumped over
the lazy whale

==> grepucase_in/foo <==
the quick
brown fox
jumped over
the lazy dog
$ head ucase_out/*
==> ucase_out/bar.out.out <==
THE LAZY WHALE

==> ucase_out/foo.out.out <==
THE LAZY DOG
```

In this case, running the workflow from the RO does not cause any errors, but the output directory is empty.