Separation of concerns

[katyhuff]

• The simulation class should only know enough to do a small number of things specific to the simulation mangement.
• The depcode class should not assume a particular depletion code choice. It should be a pure virtual class. #59
• Other classes should implement the stuff that is specific to the depletion code chosen (these should be instances (which inherit from depcode) like a serpent2 class, an openmc class, etc.)
• the geometry changing should be in its own file probably.
• the template reading and writing should be closer to the depcode class (maybe in in the serpent class).
• maybe the app class and the simulation class should be merged, then separated back out so that there is a separation of concern.

[yardasol]

Upon further inspection of the code, it seems most of these have been completed tasks. @katyhuff @andrewryh can you confirm? May need to look at the code with @munkm to verify.