Update CI workflows and add codecov.yml to avoid flaky dips in coverage

[jcurtis2]

• Manually updated/unified checkout in workflows to accommodate GitHub Node.js soon to be requirements. GitHub has transitioned its Actions runners to execute JavaScript actions using Node.js 24 by default as of June 2, 2026.
• Bump codecov version as recent PRs (Add minimal modal run to model dry deposition #211, Update PartMC to use modified version of MOSAIC_v2 #223, etc.) are failing to upload codecov data. Currently not pinned to a specific version (v6 in general) as we typically have not worried about pinning previously (even though codecov was specifically pinned to 5.5.0)
• Add codecov.yml that sets a 1% threshold on both project and patch coverage so small coverage dips don't fail CI. Additionally, there is now something in place if we want more customization.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.47%. Comparing base (e6356e7) to head (c7d2b77).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #224      +/-   ##
==========================================
+ Coverage   77.45%   77.47%   +0.02%     
==========================================
  Files          55       55              
  Lines        9420     9420              
==========================================
+ Hits         7296     7298       +2     
+ Misses       2124     2122       -2     

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