Add methods to erase time history for design optimization of transient physics

[kswartz92]

There are containers in the base physics class, e.g. time steps and checkpointed states, that need to be emptied in between design iterations. In the smith meeting on 12/14/23 possible solutions were discussed including adding reset methods for each individual entity that needs to be cleared, or added a "global" reset method that would return the base physics class to the "state" the module is in immediately following construction.

[btalamini]

Closed by #1183