_has_penetrated stores dof_id_types

Fixing stuff in contact module which used _has_penetrated.
Use PetscInt to shut up compiler when using 64-bit indices.

Update classes which override checkNonlinearConvergence() to use PetscInt.
Don't try to store max(unsigned long long) into an unsigned when all
you want is an unsigned.
MooseRandom::seed(), randl(), and rand() expect 32-bit inputs, so make sure they get it.
sorted_indices is declared as a vector<size_t> so catch its entries as size_t.