Apply repository-wide changes from pre-commit

[knoepfel]

This PR also adds the markdownlint-cli2 hook, consistent with what's in our GitHub actions.

[knoepfel]

@phlexbot markdown-fix

[github-actions]

Automatic markdownlint fixes pushed (commit f7a098c).
⚠️ Note: Some issues may require manual review and fixing.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.

@@            Coverage Diff             @@
##             main     #422      +/-   ##
==========================================
- Coverage   84.22%   84.11%   -0.11%     
==========================================
  Files         128      127       -1     
  Lines        3322     3306      -16     
  Branches      564      562       -2     
==========================================
- Hits         2798     2781      -17     
- Misses        324      328       +4     
+ Partials      200      197       -3     

Flag	Coverage Δ
unittests	84.11% <100.00%> (-0.11%)	⬇️

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Files with missing lines	Coverage Δ
plugins/python/python/phlex/_typing.py	93.65% <100.00%> (ø)

... and 4 files with indirect coverage changes

---

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[greenc-FNAL]

Does this mean we have a hysteresis brewing, if there are changes that are different to the CI?

[knoepfel]

Does this mean we have a hysteresis brewing, if there are changes that are different to the CI?

No. This means the pre-commit configuration did not include all of the checks that are in the CI.

[greenc-FNAL]

Review the full CodeQL report for details.

[greenc-FNAL]

clang-tidy failure (https://github.com/Framework-R-D/phlex/actions/runs/23065857815/job/67003882188?pr=422) should be fixed by #423.