rjl changes to support reading binary files produced by Fortran

The option output_format=='binary' was added to amrclaw and the new src/pyclaw/io/binary.py file is needed to read this in using visclaw.

Also some modifications to src/pyclaw/io/ascii.py that someone should check does not break something else in pyclaw.

In particular
 patch = solution.states[patch_index-1].patch
was replaced by
  patch = state.patch 
  
Perhaps because of a case where patches for the aux arrays were not  in the same order as patches for q arrays?