Prepare legacy checkpoint for modular simulator checkpointing

Prepare legacy checkpoint for modular simulator checkpointing

* Extend legacy checkpointing functionality to accept a CheckpointDataHolder
  for reading and writing
* Bump checkpoint version to reflect above change
* Turn off some checkpoint sanity checks when using modular simulator
* Pass CheckpointDataHolder object into checkpoint reading in runner, and
  move this object in SimulatorBuilder and then ModularSimulator for element
  setup

Refs #3517
Refs #3422
Refs #3419