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Remove scope creation from ProtectedRef module

Joe Woodward requested to merge chore/remove-unnecessary-scopes into master

What does this MR do and why?

Remove scope creation from ProtectedRef module

These scopes were used by 2 classes to fetch access levels grouped by users or groups. This polutes the other classes that inherit the ProtectedRef module and is unnecessary as we can chain the by_group or by_user scopes to fetch the same records.

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