Removed maxmx and maxmy from calling sequences 

Arrays are dynamically allocated now so we don't need to pass these around.
Many changes -- see clawpack/amrclaw/dev/fix_maxmx_notes.txt for some comments on what was done.

Someone should test that examples work. They have been converted too in examples/ directory

Attempted to change codes in src/2d/shallow/multilayer and src/2d/shallow/surge too but these have not been tested at all.

clawpack/apps codes that use geoclaw are not yet converted.