Various minor local dev/ci improvements

[TimothyWillard]

• Added code coverage check to local development via just cov as well
  as incorporating into CI by running them for python version 3.12 and
  then opting to just run the unit tests as is for other versions.
• Automatically mark tests in the tests/integration/ directory with an
  "integration" pytest marker to differentiate them and make them easier
  to run separately.
• Consolidated settings from justfile into pyproject.toml for ruff
  and mypy.
• Refactored justfile for local development UX and updated CI checks
  to do the same as local checks when possible.
• Refactored ci.yaml workflow to split code quality checks from tests.
• Updated CONTRIBUTING.md to reflect the changes made above.
• Reenabled linting/formatting/type checking/testing of code within the
  docs/ directory, which identified an issue with both the getting
  started example and the implementing a custom engine example.
  Closes Update "Approach 2: Custom build Function" section of "Creating an External Provider Package" guide #152.
• Added repo_root fixture to conftest.py for internal testing
  purposes, simplifies integration tests.
• Consolidated the steps to setup uv and just into a custom composite
  action named 'setup-just-and-uv' to DRY across the custom workflows.
  Also switched from installing just manually to using
  'extractions/setup-just@v3' to obtain a more recent version of just.

[TimothyWillard]

Follow ups:

• Consider splitting out integration tests, especially if we add more and they start taking considerably more time.
• Issues for increasing the coverage for key pieces of code currently not well covered (the simulate/skeleton/process commands, etc.)

[pearsonca]

LGTM. Per conversation - would be nice to DRY out the workflows a bit. Had one curiousity note re CONTRIBUTING doc - I think TOCs are useful, though certainly not required.

[pearsonca]

i forget: does GFM provide some auto navigation to manage this?

[TimothyWillard]

There is the toggle in the upper right of the markdown viewer that brings up the section headings (see screenshot below). Although this is probably more detailed than desired. I removed this not have duplicate tables of content on this page: https://accidda.github.io/flepimop2/latest/development/contributing/. But if you would prefer the explicit table of contents at the top of the document on GitHub I can find some other solutions.

[pearsonca]

that's what i was getting at - definitely no need for a manual TOC when Github automatically extracts.

[TimothyWillard]

Not going to re-request review for this change, but extracted out the setup for just & uv out to a composite action. Net of changes is: https://github.com/ACCIDDA/flepimop2/compare/9a83aee023df5145731589c7c6f5941a6e7070ac..e1fc745c5c29039d339d04788623618818a7e462.