Include outputs from tasks in scatters and conditionals when a workflow has no output section

[adamnovak]

This fixes #5094 by finding outputs for tasks inside control flow constructs. It should help with working around not having the workaround #5093 asks for.

This includes bumping the conformance tests with a test for this, which MiniWDL and Cromwell pass.

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.

Reviewer Checklist

• Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
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    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.
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  • New features without tests.
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Merger Checklist

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[DailyDreaming]

LGTM.