Dynamic allocation of equality engine in Theory (#4890)

Dynamic allocation of equality engine in Theory (#4890)

This commit updates Theory so that equality engines are allocated dynamically. The plan is to make this configurable based on the theory combination method.

The fundamental changes include:
- Add `d_equalityEngine` (raw) pointer to Theory, which is the "official" equality engine of the theory.
- Standardize methods for initializing Theory. This is now made more explicit in the documentation in theory.h, and includes a method `finishInitStandalone` for users of Theory that don't have an associated TheoryEngine.
- Refactor TheoryEngine::finishInit, including how Theory is initialized to incorporate the new policy.
- Things related to master equality engine are now specific to EqEngineManagerDistributed and hence can be removed from TheoryEngine. This will be further refactored in forthcoming PRs.

Note that the majority of changes are due to changing `d_equalityEngine.` to `d_equalityEngine->` throughout.