Remove db.site.lat.lon function and replace all usages with query.site

[Sweetdevil144]

Description

• query.site retrieves lat and lon.

• Removed unused db.site.lat.lon function

A small part of #3307

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 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.

[infotroph]

Thanks! This looks great. Can you please also add an entry to the NEWS.md of data.atmosphere saying that db.site.lat.lon was removed and users should use PEcAn.DB::query.site(id, con)[c("lat", "lon")] instead? Make sure to credit yourself and this PR number.