Add resave mode to check_with_errors.R

Description

Adds a new usage variant: To update the cached check results in [package_dir]/tests/Rcheck_reference.log, run the check script with env var RESAVE_CHECKS set, e.g.:

RESAVE_CHECKS=true Rscript scripts/check_with_errors.R base/db

After running, review the changes to Rcheck_reference.log and commit them if they look good.

Motivation and Context

Thanks to the whole team in general and @moki1202 in particular, lots of our cached check results are stale in the sense that they contain messages about errors/warnings we have since fixed. We've mostly been updating these by manually editing the saved files, but this is tedious and error-prone. This patch provides a one-shot method to ease the process.

As always, my hope is that we'll use this to remove fixed messages (so that we can eventually remove all Rcheck_reference.log files entirely) rather than to ignore newly added messages, but it will do either one as needed.

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 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.

PecanProject / pecan