Improve and consolidate header organization

[harrism]

Description

Fixes #1080
Depends on #1081 . This builds on #1081 but goes beyond just removing "experimental"

• Consolidate bounding_boxes APIs / headers and name files consistently
• Consolidate trajectory APIs / headers
• Consolidate distance headers
• Consolidate point-in-polygon APIs / headers and DRY up implementation

Checklist

• I am familiar with the Contributing Guidelines.
• New or existing tests cover these changes.
• The documentation is up to date with these changes.

[harrism]

This PR is superseded by #1097. Because there are so many files changed, resolving conflicts in this branch was a bit difficult.