Replace Theory::Set with TheoryIdSet (#4959)

Replace Theory::Set with TheoryIdSet (#4959)

This makes it so that equality_engine.h does not include theory.h. This is a bad dependency since Theory contains EqualityEngine.

This dependency between equality engine and theory was due to the use of a helper (Theory::Set) for representing sets of theories that is inlined into Theory. This PR moves this definition and utilities to theory_id.h.

It fixes the resulting include dependencies which are broken by changing the include theory.h -> theory_id.h in equality_engine.h.

This avoids a circular dependency in the includes between Theory -> InferenceManager -> ProofEqualityEngine -> EqualityEngine -> Theory.