Fix 404 documentation links and improve PR labeling rules (#3269, #3273)

[kutumia]

This PR addresses two improvements in the data.atmosphere module and GitHub workflows:

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Fixes for #3269 – Broken and Redirected URLs

• Replaced or commented out 404 URLs in README.md, .Rmd, and .Rd files
• Updated outdated links to Ameriflux, NEON, PEcAn documentation
• Added helpful inline comments indicating previous link status

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Fixes for #3273 – GitHub Labeler Improvements

• Refactored .github/labeler.yml to include:
  • Organized label structure (e.g., Docs/User, Scripts/R)
  • More accurate file pattern matching for automated PR labeling

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These changes improve:

• User experience with working documentation links
• Contributor workflow through more accurate PR labels
• CRAN compliance and GSoC project hygiene

Fixes: #3269
Fixes: #3273

[Sweetdevil144]

I'd say to create another PR for the PR Labeling issue as it would be much easier to trace back to the PR in case something comes up (a good practice though is generally splitting PRs for different isues). Also, would be better to confirm from @allgandalf if your changes fulfill his requirements or not?

[kutumia]

Thanks for the great suggestion — I’ve now split the original PR into two focused ones for better traceability and review:

1. Broken & outdated URLs fix: #3496 (Fixes CRAN Compliance Issue: Broken and Redirected URLs in PEcAn's data.atmosphere  #3269)

2. PR labeling improvements: #3497 (Fixes Improve PR Labeling #3273)

This should keep each discussion clean and easier to follow. I’ll also confirm with @allgandalf to ensure the labeling changes meet expectations. Appreciate your guidance!

[infotroph]

Thanks for the contribution, @kutumia! Do #3496 and #3497 replace this one fully enough it should be closed, or is there more to do here (possibly after those are merged?)