Sniffing for and workaround for keeping output of croo workflows

[adamnovak]

This is on top of #5095 and additionally fixes #5093.

Changelog Entry

To be copied to the draft changelog by merger:

• toil-wdl-runner now correctly finds and returns outputs from tasks in scatters and conditionals when a WDL workflow lacks an output section.
• toil-wdl-runner has a new --allCallOutputs option to allow including all calls' outputs in a workflow's output.
• toil-wdl-runner can now detect and try not to delete the outputs of a workflow that is meant to use the Cromwell Output Organizer (croo). Note that croo still can't actually work on the output of toil-wdl-runner.

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,cwl,wdl}.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.
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• Copy its recommended changelog entry to the Draft Changelog.
• Append the issue number in parentheses to the changelog entry.

[DailyDreaming]

This is a little odd. Especially adding an option that allows us to go against the WDL spec. We spoke about this already though, and this looks like it'll work. Thanks for adding the tests.