September cleaning 1

[cthoyt]

This PR does several bits of refactoring, but does not change any functionality. These include:

1. Better registry pattern for writers and readers
2. Remove deprecated functions long marked for deletion
3. Remove commented out imports and dead code in some places
4. Remove prints from tests, turn down logging levels when unnecessary
5. Refactoring for unnecessarily complex functions - mostly inverting the order of conditionals to avoid deep nesting, to combine multiple independent loops with itt.product
6. Refactoring to remove unnecessary back and forth conversion between lists and sets
7. Refactoring to improve variable names

[hrshdhgd]

Awesome refactor and dead-code removal @cthoyt ! Thanks a ton!