Tpetra:  Fix build error with KokkosRefactor enabled.
Stokhos:  Fix Kokkos kernels unit test for changes to Threads device.

I was calling setup, which calls Kokkos kernels, before calling
Threads::initialize().
KokkosClassic:  Add Threads::initialize() to TPINode::init().

Kokkos::Threads used to work even when Threads::intialize() wasn't
called, but that isn't the case anymore.  So I added
Threads::initialize() to TPINode::init() when KokkosCore is enabled in
KokkosClassic.  This gets the Tpetra test passing again when the Kokkos
DistObject is enabled.
fixed a couple of bugs in the new line smoothing option associated with the ordering
of equations when passing coordinates
s
MueLu: cleaned up unusued typedefs