Fixed an array range bug in Zoltan2's RCM code. The algorithm labels
all vertices -1, but then relabels all but one vertex with valid
indices. When Ifpack2's AdditiveSchwarz tries to use these indices
to perform a reordering, one of the indices may still be -1, resulting
in memory corruption. This fix causes a lot of previously failing
Tramonto tests to pass.

Build/Test Cases Summary
Enabled Packages: Zoltan2
Enabled all Forward Packages
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) INTEL_DEBUG => passed: passed=50,notpassed=0 (6.78 min)
Somehow, files for the long-deprecated and removed epetraext interface to
Zoltan reappeared in CMakeList.txt.
I am re-removing them per bug 5866.
Teuchos: Fix issue with backwards compatibility

The change to subpackages caused issues with the windows DLL testing. The fix
for the DLL testing removed a macro that is needed by one of the tests which
caused the backwards compatibility testing to complain. Since we likely aren't
going to do backwards compatibility testing on windows the need to ensure that
this macro name still exists is minimal so I am just defining it as blank to
allow the test to continue building.

Build/Test Cases Summary
Enabled Packages: TeuchosCore
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=1229,notpassed=0 (104.97 min)
1) SERIAL_RELEASE => passed: passed=1186,notpassed=0 (49.78 min)
Updating rc and dev versions (not release).
Added removeDirIfExists() helper (Trilinos #5856)

This will be used for implementing removal of CMakeFiles/ (Trilinos #5856).
Adding removal of CMakeFiles/ before configure (Trilinos #5856)

I added a new very strong unit test that ensures that the CMakeCache.txt and
the CMakeFiles directory get removed correctly before a configure.

The way I wrote the test, I ensure that the removal of these files only occurs
before a configure if they already exist and only if the the configure is
actually attempted and do not get removed otherwise.  The only aspect I don't
test it to ensure that CMakeCache.txt and CMakeFiles get removed *before* the
reconfigure takes place.  However, that defect seems very unliklely to be
added in the future.

Note that before I had not tests to ensure that the CMakeCache.txt file was
getting removed correctly.

Build/Test Cases Summary
Enabled Packages: TrilinosFramework
Disabled Packages: CTrilinos,ForTrilinos,PyTrilinos,Didasko,Mesquite,Phdmesh,Pliris,Claps
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=102,notpassed=0 (1.78 min)
1) SERIAL_RELEASE => passed: passed=102,notpassed=0 (1.08 min)
Other local commits for this build/test group: 3cbdc72, d86ca41
SEACAS: grepos - detect bad (unsupported) node merge command

(From Sierra)
IOSS: Fix bounding box for 1d, 2d models (thanks to v brunini for catching)

(From Sierra)

Build/Test Cases Summary
Enabled Packages: SEACASGrepos, SEACASIoss
Disabled Packages: Panzer,PyTrilinos
Enabled all Forward Packages
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=21,notpassed=0 (24.65 min)
3) SERIAL_RELEASE_SS => passed: passed=22,notpassed=0 (27.18 min)
Other local commits for this build/test group: cda05a4
Addressing Windows 64 bit Intel std::abs(ptrdiff_t) issue (Trilinos #5856)

This should fix the compile issue reported by Jordan L. as part of the SCALE
Windows 64 bit Intel C++ build (see Trilnos #5856).

There as no code in RTOp or Thyra that covered this function so I added a unit
test to check it before making the change (i.e. the Legacy Software Change
Algorithm).  I think this never came up before because SCALE is the only
Trilinos customer that I know that is using 64 bit Intel C++ on Windows with
Trilinos.  God bless them!

Build/Test Cases Summary
Enabled Packages: RTOp, Thyra
Disabled Packages: CTrilinos,ForTrilinos,PyTrilinos,Didasko,Mesquite,Phdmesh,Pliris,Claps
0) MPI_DEBUG => passed: passed=72,notpassed=0 (17.74 min)
1) SERIAL_RELEASE => passed: passed=73,notpassed=0 (2.85 min)
Fixing uninitialized variable warning.
Fixing projection of coordinates.

Coordinates were being projected with R.  However, because rows of R are normalized, the scaling of the
projected coordinates was off.  This in turn cause the graph partitioner to redistribute the matrix
poorly, which in turn broke the aggregation.

Big thanks to Chris Siefert to helping to track this down.
Fixing nnz per row output in smoother summary.
Adding control over debugging output from Zoltan.
Stashing mx and my on parameter list.

This allows the calling program to find out how Galeri has distributed the problem
Synchronizing Galeri coordinate generation.

Now coordinates should match between Epetra and Tpetra.

Build/Test Cases Summary
Enabled Packages: Galeri, ML, MueLu
Disabled Packages: MOOCHO
Enabled all Forward Packages
0) MPI_DEBUG => passed: passed=389,notpassed=0 (28.78 min)
1) SERIAL_RELEASE => passed: passed=363,notpassed=0 (12.69 min)
2) MPI_SS_DEBUG => passed: passed=198,notpassed=0 (13.23 min)
Other local commits for this build/test group: 963d245, 7b127ff, bc17101, 5dc4fb8, de81890
Provide for batch indenting of C/C++ files based on emacs 'thyra' style

The 'thyra' emacs style is very good for development work to automatically
indent C++ code just by hitting 'tab' or running the 'inden-region' function.
In order to allow for automatic indentation of a source file (perhaps as a git
commit hook), it would be nice to be able to do this auotmatically in batch mode.

That is what this little emacs Lisp function can do when run in emacs batch
mode.  I tried this out and it works.

I ran this on a large Tpetra file as:

$ time emacs -batch Tpetra_CrsMatrix_def.hpp \
  -l <THIS_DIR>/batch-indent-file -f emacs-format-function
...
real	1m4.435s
user	1m4.337s
sys	0m0.080s

This worked to indent the file but it took a very long time.  That is not
good.  This is not a viable way to write any type of git commit hook to fix
the indentation of source files.  At the very best I could use this to fix the
formatting on a bunch of files in batch mode offline.

In any case, I am committing this simple script to the Trilinos git repo in
any case so that I can use it in the future if I need to and to document this
some.
change timer message from log_debug() to log_info().
is_any_wr_complete() - fix improper use of 'const gni_work request **'.  remove const.
is_all_wr_complete() - fix improper use of 'const gni_work request **'.  remove const.
remove attempts to work around conflicts between "gcc -ansi -pedantic" and rpcgen output.
instead, add grep/perl to the rpcgen pipeline to filter out the conflicts.
remove attempts to work around conflicts between "gcc -ansi -pedantic" and rpcgen output.
instead, rely on TriosProcessXDR.cmake to fix these conflicts.
add copyright header where missing.