Update actions/checkout to v6, upload-artifact to v7, codecov/codecov-action to v6, and actions/upload-pages-artifact to v5, actions/cache to v5

[remlapmot]

This

• updates actions/checkout to v6 in the examples and READMEs
• updates actions/checkout to its v6.0.2 commit in the Makefile and workflows
• updates actions/upload-artifact to v7
• updates actions/upload-artifact to its v7.0.1 commit in the Makefile and workflows
• updates codecov/codecov-action to v6
• updates codecov/codecov-action to its v6.0.0 commit in the Makefile and workflows, and then makes the minor update to the .github/workflows/test-coverage.yaml workflow
• updates actions/upload-pages-artifact to v5
• updates actions/cache to v5 in the examples and READMEs and bumps actions/cache/save and actions/cache/restore to v5
• refreshes the list of macos runners in .github/workflows/setup-pandoc-test.yaml
• adds two missing files to .Rbuildignore
• updates actions in .github/workflows/scorecard.yml
• updates dessant/lock-threads to v6.0.0

Closes #1042

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.61%. Comparing base (6f6e5bc) to head (03276b1).

Additional details and impacted files

@@            Coverage Diff             @@
##           v2-branch    #1014   +/-   ##
==========================================
  Coverage      84.61%   84.61%           
==========================================
  Files              3        3           
  Lines             13       13           
==========================================
  Hits              11       11           
  Misses             2        2           

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[remlapmot]

Sorry this got big - but many actions have new versions - and if you leave it longer the situation will just get worse.

Would you have time for a review @gaborcsardi ?

[CGMossa]

Can this be done soon?

Warning: Node.js 20 actions are deprecated. The following actions are running on Node.js 20 and may not work as expected: actions/cache@v4, mozilla-actions/sccache-action@v0.0.9, r-lib/actions/setup-r@v2. Actions will be forced to run with Node.js 24 by default starting June 2nd, 2026. Node.js 20 will be removed from the runner on September 16th, 2026. Please check if updated versions of these actions are available that support Node.js 24. To opt into Node.js 24 now, set the FORCE_JAVASCRIPT_ACTIONS_TO_NODE24=true environment variable on the runner or in your workflow file. Once Node.js 24 becomes the default, you can temporarily opt out by setting ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION=true. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

[gaborcsardi]

Can this be done soon?

The deprecation is more than a month away, why is this urgent for you?

[CGMossa]

it is not urgent; this pr was made on Aug 13, 2025. it is fairly involved, especially with things I am unfamiliar with. so soon can be whatever is appropriate. a month to review this is soon.