Packing Error: relative path to tools are falsely handled as absolute

## Expected Behavior
https://raw.githubusercontent.com/CompEpigen/ATACseq_workflows/1.2.0/CWL/workflows/ATACseq.cwl succeeds validation:

`cwltool --validate https://raw.githubusercontent.com/CompEpigen/ATACseq_workflows/1.2.0/CWL/workflows/ATACseq.cwl`

Therefore, packing should work without problems.

## Actual Behavior
`cwltool --pack --debug https://raw.githubusercontent.com/CompEpigen/ATACseq_workflows/1.2.0/CWL/workflows/ATACseq.cwl` fails.

## Workflow Code
```
https://raw.githubusercontent.com/CompEpigen/ATACseq_workflows/1.2.0/CWL/workflows/ATACseq.cwl
```

## Full Traceback
```pytb
INFO /usr/local/bin/cwltool 2.0.20200124134010
ERROR Tool definition failed validation:
[Errno 2] No such file or directory: '/mnt/c/Users/kerst/OneDrive/tools/bedtools_bedtobam.cwl'
Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 198, in fetch_text
urllib.request.url2pathname(str(path)), encoding="utf-8"
FileNotFoundError: [Errno 2] No such file or directory: '/mnt/c/Users/kerst/OneDrive/tools/bedtools_bedtobam.cwl'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/usr/local/lib/python3.6/dist-packages/cwltool/main.py", line 916, in main
print_pack(loadingContext.loader, processobj, uri, metadata)
File "/usr/local/lib/python3.6/dist-packages/cwltool/main.py", line 563, in print_pack
packed = pack(document_loader, processobj, uri, metadata)
File "/usr/local/lib/python3.6/dist-packages/cwltool/pack.py", line 151, in pack
find_run(processobj, loadref, runs)
File "/usr/local/lib/python3.6/dist-packages/cwltool/pack.py", line 57, in find_run
find_run(s, loadref, runs)
File "/usr/local/lib/python3.6/dist-packages/cwltool/pack.py", line 50, in find_run
find_run(s, loadref, runs)
File "/usr/local/lib/python3.6/dist-packages/cwltool/pack.py", line 55, in find_run
find_run(loadref(None, d["run"]), loadref, runs)
File "/usr/local/lib/python3.6/dist-packages/cwltool/pack.py", line 57, in find_run
find_run(s, loadref, runs)
File "/usr/local/lib/python3.6/dist-packages/cwltool/pack.py", line 57, in find_run
find_run(s, loadref, runs)
File "/usr/local/lib/python3.6/dist-packages/cwltool/pack.py", line 55, in find_run
find_run(loadref(None, d["run"]), loadref, runs)
File "/usr/local/lib/python3.6/dist-packages/cwltool/pack.py", line 145, in loadref
return document_loader.resolve_ref(uri, base_url=base)[0]
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 735, in resolve_ref
doc = self.fetch(doc_url, inject_ids=(not mixin))
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 1194, in fetch
text = self.fetch_text(url)
File "/usr/local/lib/python3.6/dist-packages/schema_salad/ref_resolver.py", line 204, in fetch_text
raise ValidationException(str(err)) from err
schema_salad.exceptions.ValidationException: [Errno 2] No such file or directory: '/mnt/c/Users/kerst/OneDrive/tools/bedtools_bedtobam.cwl'
```

If I understand the error correctly, the relative tool reference `../tools/bedtools_bedtobam.cwl` (see [here](https://github.com/CompEpigen/ATACseq_workflows/blob/master/CWL/workflow_modules/bed_to_coverage_track.cwl#L33)) gets converted into a non-existing absolute path `/mnt/c/Users/kerst/OneDrive/tools/bedtools_bedtobam.cwl` (with `/mnt/c/Users/kerst/OneDrive/` being the parent of my working directory).

Of note, `../tools/bedtools_bedtobam.cwl` is referenced in a [sub-workflow](https://github.com/CompEpigen/ATACseq_workflows/blob/master/CWL/workflow_modules/bed_to_coverage_track.cwl) which is in another directory than the [main workflow](https://github.com/CompEpigen/ATACseq_workflows/blob/master/CWL/workflows/ATACseq.cwl#L209). Maybe, this has something to do with the error.

## Your Environment
* cwltool version: 2.0.20200124134010 (from current master branch)

With the older version 1.0.20180809224403 the workflow packs as expected.