Make Pip willing to hide system Python modules

[adamnovak]

This hides system Python modules when Toil needs a newer version. This should fix #5320.

This should mostly be fine except when the Toil docker uses the system standard Python version, when it is not fine at all and might break system components like software-properties-common.

The real solution is to migrate from system Toil and --system-site-packages for user venvs, to a main Toil venv and .pth files to connect it to user venvs, but that requires Toil changes to understand which venvs it should hot-deploy and which it shouldn't.

Changelog Entry

To be copied to the draft changelog by merger:

• Toil Docker build is now willing to hide system Python packages
• Toil Docker container no longer ships s3am by default.

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 passed tests, including the Gitlab tests, for the most recent commit in its branch.
• Make sure the PR has been reviewed. If not, review it. If it has been reviewed and any requested changes seem to have been addressed, proceed.
• 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.

[stxue1]

This seems okay since this is just a temporary solution until #5322