Changes we need to incorporate in 3d

Things added to 2d amrclaw that haven't made it into 3d:

• Python interface for input parameters -- hold off until 5.0?
• Python plotting routines
• gauges -- Kirsten added this to 3d at one point, need to find.
• anisotropic refinement in time -- not high priority but might be nice eventually
• NetCDF output option
• Interleaving arrays (reordering indices), which is only in the branch reordered_4.x of 2d amrclaw now

Things we've added to GeoClaw that haven't yet made it into 2d (or 3d) amrclaw:

• fixed grid output
• possibility of specifying "regions" where refinement is allowed or required