Add toil debug-job tutorial

[adamnovak]

This will fix #4894 by adding another tutorial to the debugging page. The tutorial shows using toil debug-job to sneak inside a Docker container locally and inspect the behavior of a stuck WDL task.

It also includes fixes I needed for problems I encountered when trying to write a workflow that failed the way I wanted instead of in other ways. I was stuck for quite a while because my Docker Desktop installation had decided to change its file sharing mode without telling me.

Changelog Entry

To be copied to the draft changelog by merger:

• Toil documentation now has a tutorial on a more real-world usage of toil debug-job
• toil debug-job now leaves behind the worker's temp files after running, so you can look at them.
• Worker logs to leader and user streams (like WDL task standard error) are now sent to the leader even if the job failed.
• Toil installation instructions now cover the required configuration of Mac Docker Desktop.
• WDL Docker containers now check to make sure input files are not unexpectedly truncated.

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.
  • [ ] 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.