Consolidate Region Specifications and Simplify Flagging Routine

[mandli]

Remove level restrictions for topograpy, dtopography, and qinit in favor of just specifying regions. A check would be made to see if a point was in any of the remaining regions and if it was not would be generally allowed to be flagged. This would imply that regions would then have to be specified in the same locations for a given topography for instance to gain the same functionality as before. This can more than likely be taken care of in the python class that implements this behavior.

[rjleveque]

Note that $CLAW/amrclaw/src/2d/flagregions2.f90 appears to flag based on regions and so does $CLAW/geoclaw/src/2d/shallow/flag2refine.f90. @mjberger: Are both being used?

Also some geoclaw/example Makefiles include both flagregions2.f90 and flagregions.f and should be cleaned up. The latter doesn't even exist although there is still a deprecated flagregions.f90.

[mandli]

In GeoClaw then are we checking for regions twice then?