Formalize N-step initialization

[hrajagers]

Use cases:

• Set MPI_COMMUNICATOR before initialize
• Change model settings (e.g. add sources/sinks, simulation quantities) and then initialize those arrays and subsequently set the values

[mdpiper]

Another use case:

• Perform model calculations valid at initial time step

(This is a request from @sc0tts.)

[ipelupessy]

this needs #22.