Invalid --pack results if input and output have the same name in a referred CWL

In a single CWL, input and output names can be the same, however, it seems not the case in a referred CWL when using `--pack`.
I attached a mini repository to illustrate the issue: https://github.com/EmileSonneveld/cwltool-pack-bug
In the last commit you can see that I made the input and output variables match name, and `--pack` gives a different result.

We use calrissian to run various CWLs. Pack would help use to avoid errors further in the workflow.

Start with the attached cwltool-pack-bug repository and reproduce the differing result from the --pack entry point when a referred CWL uses the same input and output name. Trace how packing handles those referenced names; done means the packed CWL preserves the valid same-name behavior seen in the single CWL case.

Written by the indexing model from the issue text.