Provenance: fix bagit structure when there are no data files

[simleo]

When the workflow has no input or output files, the RO created by cwltool --provenance has no files under data/. In this case, no bagit manifest is created, making the RO bag invalid:

from bdbag.bdbagit import BDBag

bag = BDBag("ro")
bag.validate()

bagit.BagValidationError: No manifest files found

This PR changes ResearchObject so that it creates an empty manifest to fix the bagit structure in such cases.

[codecov]

Codecov Report

Merging #1727 (49b44e5) into main (49b44e5) will not change coverage.
The diff coverage is n/a.

❗ Current head 49b44e5 differs from pull request most recent head 54539b6. Consider uploading reports for the commit 54539b6 to get more accurate results

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  Files          89       89           
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  Hits        10556    10556           
  Misses       4201     4201           
  Partials     1089     1089           

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