Consider moving the DofHandler into Geometry

[stvdwtt]

Right now a lot of the functionality involving the "geometry" of the problem has to be in ThermalPhysics since that's where the DofHandler is. Conceptually this is a little confusing, but more importantly, it could lead to duplication if there are multiple Physics objects in a single calculation. We should look into moving DofHandler into Geometry so we can centralize some of this functionality.

This probably makes sense to push off until we have more of the functionality implemented so that we have a better idea of what should be put where.