Refactor how assertions are added to decision engine (#2396)

Refactor how assertions are added to decision engine (#2396)

Before refactoring the preprocessing passes, we were using three
arguments to add assertions to the decision engine. Now all that
information lives in the AssertionPipeline. This commit moves the
AssertionPipeline to its own file and changes the `addAssertions()`
methods related to the decision engine to take an AssertionPipeline as
an arguement instead of three separate ones. Additionally, the
TheoryEngine now uses an AssertionPipeline for lemmas.