default values of "class: File" or "class: Directory" need persisting

[mr-c]

and their location fields updated with a Galaxy URI

can be discovered via cwltool --print-deps ~/common-workflow-language/v1.0/v1.0/count-lines11-extra-step-wf-noET.cwl or directly via cwltool.main.find_deps (see also cwltool.main.printdeps)

[mr-c]

This is how Arvados does this https://github.com/arvados/arvados/blob/main/sdk/cwl/arvados_cwl/runner.py#L241

Probably could refactor that and we could pull it into cwltool with a callback for uploading