Stokhos:  Updated for Kokkos Host -> Threads refactor.
Kokkos(linalg): Adding a replace values to the CrsMatrix

This is basically a copy of the sum method, but uses an atomic
exchange instead
Add additional Kokkos files to needed files for Sierra

The KokkosCore_config.h is needed to build part of Sierra
Adding X permission to avoid find for x files and dirs

Will be faster and do the same thing.
Updating unit tests for changes in Fortran flags in commit 12d21f4

Back in commit 12d21f4 I added the general language flags for C and C++ to
Fortran so that -g would be added to the compiler flags for Fortran as well.
Fortran is code that needs to be debugged too.  This commit here just updates
the unit tests to be consistent with that change.

Note that this change will also result in -D_GLIBCXX_DEBUG being added to
CMAEK_Fortran_FLAGS when STL checking is enabled.  Adding this define to
Fortran makes no sense but it should be harmess for gfortran.  I think almost
all Fortran compilers accept preprocessor defines through -D.  In any case,
these options are only added if the compiler matches as 'GNU' in CMake.

Build/Test Cases Summary
Enabled Packages: TrilinosFramework
Disabled Packages: CTrilinos,ForTrilinos,PyTrilinos,Didasko,Mesquite,Phdmesh,Pliris,Claps
0) MPI_DEBUG => passed: passed=109,notpassed=0 (2.93 min)
1) SERIAL_RELEASE => Test case SERIAL_RELEASE was not run! => Does not affect push readiness! (-1.00 min)
Kokkos: Map thread teams onto a virtual league so that a parallel operation can request more teams than actually exist.
Kokkos: Improve Threads::initialize documentation.
Getting rid of the old setup function, adding a few parameters for Additive Schwarz,
setting smoother/coarse grid solver factories to null for the first setup stage,
and updating examples.

Build/Test Cases Summary
Enabled Packages: MueLu
0) MPI_DEBUG => Skipped configure, build, test due to no enabled packages! => Does not affect push readiness! (-1.00 min)
1) SERIAL_RELEASE => Skipped configure, build, test due to no enabled packages! => Does not affect push readiness! (-1.00 min)
2) MPI_DEBUG_SS => passed: passed=35,notpassed=0 (1.55 min)
Panzer: Keying the type of Ordinal64 off Teuchos_ENABLE_LONG_LONG
Removed incorrect doxygen comments.
I don't know what task_communication_adj and task_communication_xadj are,
but I know they aren't what the comment said they were.
Merge branch 'master' of software.sandia.gov:/space/git/Trilinos
MueLu: nightly coverage for experimental flag

Runs on eleanor.
Increase timeout limit for a few builds
Trilinos: Update flat header directory.

(From Sierra)
Trilinos: Update flat header directory.

(From Sierra)
MueLu: fix nightly experimental test script

Fixing capitalization typo.
MueLu_ENABLE_Experimental requires Xpetra_ENABLE_Experimental.
=Added a Cholmod Adaptor to amesos2 and a support graph preconditioner to Ifpack2, both remain in experimental
=added a flag to make sure Ifpack_Supportgraph2 would only be included when enabled

Build/Test Cases Summary
Enabled Packages: TrilinosFramework, Amesos2, Ifpack, Ifpack2
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=545,notpassed=0 (17.41 min)
1) SERIAL_RELEASE => passed: passed=401,notpassed=0 (4.74 min)
Other local commits for this build/test group: 8cce5bc
Kokkos: Adding md_skeleton usecase for Trilinos tutorial

Christian
Merge branch 'master' of software.sandia.gov:/space/git/Trilinos