Allow filestore bypass

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• --bypass-file-store lets toil-cwl-runner support inplaceUpdateRequirement

Reviewer Checklist

• Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
  • If it is coming from an external repo, make sure to pull it in for CI with:

    contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
    

  • If there is no associated issue, create one.
• Read through the code changes. Make sure that it doesn't have:
  • Addition of trailing whitespace.
  • New variable or member names in camelCase that want to be in snake_case.
  • New functions without type hints.
  • New functions or classes without informative docstrings.
  • Changes to semantics not reflected in the relevant docstrings.
  • New or changed command line options for Toil workflows that are not reflected in docs/running/cliOptions.rst
  • New features without tests.
• Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
• Finish the review with an overall description of your opinion.

Merger Checklist

• Make sure the PR passes tests.
• Make sure the PR has been reviewed since its last modification. If not, review it.
• Merge with the Github "Squash and merge" feature.
  • If there are multiple authors' commits, add Co-authored-by to give credit to all contributing authors.
• Copy its recommended changelog entry to the Draft Changelog.
• Append the issue number in parentheses to the changelog entry.

[adamnovak]

OK @DailyDreaming, I've written a better message that explains what you should need to get InplaceUpdateRequirement working.

[DailyDreaming]

@adamnovak Thanks. This looks good to me, provided the comments in the PR this is based on are addressed (#3628).

[adamnovak]

When this is finally done it will probably fix #3667.