[24.0] Don't fail metadata if we only have an extra output files dir

[mvdbeek]

This used to be fine in some deployments, and not in others. I think this is fine, considering we got the extra output files dir the job completed successfully. We expect this for composite datasets with auto_primary_file, but other cases like directory datatypes could also be doing this.

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[mvdbeek]

I've deployed this to main already and it fixes galaxyproject/usegalaxy-tools#731