Tweaks to order and domain

As of this commit the ike run is running at 5 levels of refinement.
Merge remote branch 'mandli/rm-layer-density' into rm-layer-density
Merge remote branch 'mandli/rm-layer-density' into rm-layer-density

Conflicts:
	examples/storm_surge/gulf/ike/setrun.py
Add more info to CFL violation, fix setrun bugs