[24.2] Prefer our package index server

[nsoranzo]

when running tests with tox that install dependencies from requirements.txt files.

Workaround for astral-sh/uv#7496 .

Fix the mypy and test_galaxy_packages tests on Python 3.13 CI workflows, which have started to fail to build the pysam wheel, e.g.: https://github.com/galaxyproject/galaxy/actions/runs/12217240928/job/34081246419

Backported from #19282 .

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[nsoranzo]

Test failures unrelated.