Update of petscdiff and associated harness hooks

Changes to petscdiff:
 o Changes -u flag to -m flag to avoid conflicts with diff
 o Adds a -j flag which does an simple diff
 o Adds a -J flag which then uses diff with specified arguments

 petsc_harness.sh and gmakefile were then updated to use the -m
 flag with REPLACE=1 to gmakefile, and use the -j flag with
 DIFF_NUMBERS=1 to gmakefile.