(proof-new) Preprocessing passes use proper interfaces to assertions pipeline (#5164)

(proof-new) Preprocessing passes use proper interfaces to assertions pipeline (#5164)

This PR eliminates all uses of assertions pipeline that are not proper, which two-fold:
(1) The assertion list should never be modified in a custom way (without going through replace / push_back),
(2) Places where an assertion is "conjoined" to an existing spot in the vector should use conjoin instead of replace.
This is required for proper proof generation.

This fixes CVC4/cvc4-projects#75.