Reproduce docker image fixes (pinning versions) from SWE-Bench

[nielstron]

This pre-emptively reproduces some of the PRs reported at SWE-bench for lacking pinned versions. List, to be updated:

• pallets__flask-4045
• sphinx-doc__sphinx-11445

TODO:

• https://github.com/princeton-nlp/SWE-bench/pull/184
• https://github.com/princeton-nlp/SWE-bench/pull/232 and https://github.com/princeton-nlp/SWE-bench/pull/236