Workflow fails validation after packing

## Expected Behavior
The workflow https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl passes validation. This should not change after packing.

## Actual Behavior
`cwltool --validate "https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl"` --> valid

`cwltool --pack "https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl" > packed.cwl` --> no exceptions

`cwltool --validate packed.cwl` --> packed.cwl fails validation with the error given below.

## Workflow Code
```
https://raw.githubusercontent.com/Athanaseus/2gc-pipeline/master/selfcal_simulation.cwl
```

## Full Traceback
```pytb
INFO /usr/local/bin/cwltool 2.0.20200124134010
INFO Resolved 'test.cwl' to 'file:///mnt/c/Users/kerst/OneDrive/home/test.cwl'
ERROR Tool definition failed validation:
test.cwl:3:9: checking object `test.cwl#bdsf_fits2lsm.cwl`
test.cwl:5:13: checking field `requirements`
test.cwl:23:17: checking item
Field `class` contains undefined reference to
`file:///mnt/c/Users/kerst/OneDrive/home/InplaceUpdateRequirement`
test.cwl:70:9: checking object `test.cwl#cubical.cwl`
test.cwl:72:13: checking field `requirements`
test.cwl:91:17: checking item
Field `class` contains undefined reference to
`file:///mnt/c/Users/kerst/OneDrive/home/InplaceUpdateRequirement`
test.cwl:2342:9: checking object `test.cwl#pybdsf.cwl`
test.cwl:2344:13: checking field `requirements`
test.cwl:2361:17: checking item
Field `class` contains undefined reference to
`file:///mnt/c/Users/kerst/OneDrive/home/InplaceUpdateRequirement`
test.cwl:3030:9: checking object `test.cwl#simulator.cwl`
test.cwl:3032:13: checking field `requirements`
test.cwl:3045:17: checking item
Field `class` contains undefined reference to
`file:///mnt/c/Users/kerst/OneDrive/home/InplaceUpdateRequirement`
test.cwl:3176:9: checking object `test.cwl#tigger_convert.cwl`
test.cwl:3178:13: checking field `requirements`
test.cwl:3183:17: checking item
Field `class` contains undefined reference to
`file:///mnt/c/Users/kerst/OneDrive/home/InplaceUpdateRequirement`
test.cwl:3571:9: checking object `test.cwl#wsclean.cwl`
test.cwl:3573:13: checking field `requirements`
test.cwl:3586:17: checking item
Field `class` contains undefined reference to
`file:///mnt/c/Users/kerst/OneDrive/home/InplaceUpdateRequirement`
```

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