Hide data in Domain

[btalamini]

Following up on Mike's comment: this changes Domain from a struct to a class, with the expected hiding of internal data.

[tupek2]

Looks good to me, seems like we need to get that new formatting in. Its going crazy on these files.

[btalamini]

Looks good to me, seems like we need to get that new formatting in. Its going crazy on these files.

I agree. In particular, the forced alignment of the right side of = assignments triggers changes to lines that weren't touched by the PR, making the PR bigger, and more difficult to review, since you have to read closely to see if the change is substantial or style.

[btalamini]

Let's hold this back until I get the boundary condition PR in. I'll handle the conflicts that emerge in this PR later.