Fix for #2968 to add `write` argument to `get.trait.data()` and friends

[Aariq]

Description

Adds a write argument to get.trait.data() and get.trait.data.pft() and changes runModule.get.trait.data() and get.trait.data() to correctly pass the write argument. Minor fixes to documentation, code formatting, and fixed one unrelated check warning in site.pft.link.settings()

Motivation and Context

Closes #2968

Review Time Estimate

• [ ] Immediately
• [ ] Within one week
• [ ] When possible

Types of changes

• [x] 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.
• [x] My name is in the list of CITATION.cff
• [x] I have updated the CHANGELOG.md.
• [x] I have updated the documentation accordingly.
• [x] I have read the CONTRIBUTING document.
• [ ] I have added tests to cover my changes.
• [ ] All new and existing tests passed.

[Aariq]

Should I add a NEWS.md to the settings package and bump the version?

[Aariq]

Looks like test coverage for these functions is 0%, but I did install this PR and test with an existing run and the behavior is correct. Not sure how to write tests for database stuff, but I can try if you'd like.