WIP: Fix and standardize @examples (\dontrun{})

[S1DDHEY]

Description

fixes #3797
This WIP PR starts cleaning up Roxygen @examples across PEcAn packages.

So far this includes:

• Fixing syntactic errors that cause pkgdown example parse failures
• Making examples self-contained (no undefined symbols)
• Converting non-R commands inside @examples to comments
• Standardizing use of \dontrun{} vs \donttest{} based on side effects

Motivation and Context

Review Time Estimate

• Immediately
• Within one week
• When possible

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

• My change requires a change to the documentation.
• My name is in the list of CITATION.cff
• I agree that PEcAn Project may distribute my contribution under any or all of
  • the same license as the existing code,
  • and/or the BSD 3-clause license.
• I have updated the CHANGELOG.md.
• I have updated the documentation accordingly.
• I have read the CONTRIBUTING document.
• I have added tests to cover my changes.
• All new and existing tests passed.

[S1DDHEY]

I've added most of changes to @examples here, only the make document step remains to update the .Rd files which I'll do after this is reviewed.

There are also a few functions whose examples require specific inputs or domain knowledge that I don’t currently have. For those, I plan to open a separate issue.