Cleanup of warnings for more specific issues

Passes test suite

Cross Stream Shear was removed from post processing as it had negative indexing into arrays, and was recommended not to be used since 2/9/02 in Goma Manual

Makefiles updated to use trilinos as a system library (-isystem) and on the main Makefile to remove -Wall flag from FFLAGS

MAX_CONC checking was added to some problems that expect to be able to index to a specific amount in arrays that are defined using MAX_CONC

In the setup_Elem_BC an array was using MAX_NODES_PER_SIDE but was always using num_nodes_on_side to index in all functions that the array was used, and as this was causing a warning I changed the array size to be num_nodes_on_side.