Restructured meumapps-ss implementation code and the SS class

Addresses #30 (closed)

I'm not sure if the skeleton is a bit overkill or not. I'm not sure if we need an initialize, finalize, pre-time step, and post-time step methods. If it turns out that any of those are just a few lines, we can eliminate that method and just put those lines in run().

I'm still not 100% on what should be in the constructor and what should be in initialize. Let's just try to have a sensible breakdown and we can refactor later. If I remember correctly, @4pf was saying that there were some limitations about what we could do in the constructor once we add a base class.

The default input file is for a pretty big problem 320^3. That crashes on my laptop due to memory constraints. I created a new input file for integration testing with a 32^3 domain (and a few other changes like reducing the number of time steps and the number of particles).