Refactor ExtractsRef to use RefExtractor logic

What does this MR do and why?

Contributes to #425379

ExtractsRef module is included into Rails controllers, that call some methods from this class. This dependency is not clear and couples controller logic to this module.

The main goal is to transition from implicit calls of ExtractsRef module methods in Rails controller, to use ExtractsRef::RefExtractor class that contains this logic. As a final step we will delete ExtractsRef and ExtractsPath modules completely.

Previously,

1. Code from ExtractsRef module was copied to ExtractsRef::RefExtractor class (See !131125 (merged))
2. Some duplications were removed: !152068 (merged)

This MR:

1. Replaces implicit #extract_ref calls with ExtractsRef::RefExtractor
2. Removes old/unused code from ExtractsRef module