CWLProv: no trace of secondaryFiles for workflow activity

[simleo]

See grepsort-run-1 (generated with an older cwltool version, but I've verified the problem is still present in version 3.1.20230624081518). The problem is that a cwlprov:SecondaryFile record is generated only for the activity corresponding to the relevant tool run (greptool.cwl), but not for the activity corresponding to the workflow run. In runcrate, the result is that the workflow action ends up being assigned a single file as input instead of a Collection of the single file + the secondary file, so after parameter conversion is done this hack is run to replace it with the Collection generated for the tool run. The hack, however, does not work if different landing directories are used for different activities (see this comment).