`cwltool --pack` has trouble with relative paths in second level linked files

The following workflow `https://github.com/genome/analysis-workflows/blob/master/definitions/pipelines/bisulfite.cwl` has a linked sub-workflow `https://github.com/genome/analysis-workflows/blob/master/definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl` which has a linked tool `https://github.com/genome/analysis-workflows/blob/master/definitions/tools/bam_to_fastq.cwl`

```
cwltool --pack pipelines/bisulfite.cwl
INFO /Users/kghose/.venvs/cwltool/bin/cwltool 2.0.20200126090152
INFO Resolved 'pipelines/bisulfite.cwl' to 'file:///Users/kghose/Work/code/benten/tests/cwl/mgi/pipelines/bisulfite.cwl'
ERROR Tool definition failed validation:
[Errno 2] No such file or directory: '/Users/kghose/Work/code/benten/tests/cwl/tools/bam_to_fastq.cwl'
```

Seems like this second level relative file path confuses `cwltool --pack`

```cwltool --version
2.0.20200126090152
```