MAINT: clean-up utils

There is a lot of historical baggage in `utils`, and it would be great to do an audit and refactor+cleanup to remove unnecessary functionality.
Also, add the note to the docs that `utils` is for internal usage, we shouldn't be forced to do long deprecations.

Start by locating the repository's utils code and documentation, then audit the existing utilities for historical or unnecessary functionality. Define the cleanup scope before changing anything, and document that utils is for internal use. Done means the agreed obsolete functionality is removed and the usage note is present.

Written by the indexing model from the issue text.