Behavior of `cwltool --pack` is inconsistent when tool has an ID

[jdidion]

The typical behavior of cwltool --pack is to set the ID of the main tool/workflow to #main and then prefix all it's input and output IDs with #main/. However, when the tool defines id then the input and output IDs don't get the prefix even though the name of the tool is changed to #main. When I remove the tool id the generated file is as expected. This can be reproduced by trying to pack https://github.com/common-workflow-language/cwl-v1.2/blob/main/tests/stage_file_array.cwl with and without the tool id field.

[mr-c]

Confirmed. Same as #1470 ; related to #1436