[WIP] Regions in 3D

[cjvogl]

Implementation of regions via flag2refine.

[rjleveque]

Thanks @cjvogl, but I suggest we hold off on this for the 5.4.0 release. In 2d there is a separate flagregions.f90 file, since flag2refine might not be used if the user specifies Richardson error estimation for the flagging, and we probably want to do something consistent.

I think we also need to modify the utilities so that setrun.py can specify regions?

[cjvogl]

Works for me @rjleveque. I believe all the changes to the utilities were taken care of in #169 (just making a note of this so I can remember down the road).

[rjleveque]

Thanks for the reminder! Let's work more on this soon, along with the slices output and other 3d enhancements.