Fixes for 64bit indices

This branch gets MOOSE compiling and running when PETSc is configured with `--with-64-bit-indices=1`, and libmesh is configured with `--with-dof-id-bytes=8`.

This commit *shouldn't* break anything for anyone using 32-bit indices, it's basically enforcing consistent use of `dof_id_type` over `unsigned int` where necessary.  By the same token, new invalid uses of `unsigned int` will probably continue to creep into the code unless we're really vigilant, so it might be worth creating a "big indices" build target going forward...

Refs #4321.