Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComp

Merge branch 'master' into knepley/feature-plex-parallel-submesh

* master: (2931 commits)
remove N in docs for SNESQN
replaced test tolerance with PETSC_SQRT_MACHINE_EPSILON
fortran: PetscComplex type is missing from fortran
initialize variables so that static analyzer doesn't mistakenly think they are used uninitialized.
Move access of prefix until it is actually used
Remove DMDASplitComm2d(), used in one example that was not tested
Functions that do not return PetscErrorCode should not use PetscFunctionBegin/End paradgm
remove unneeded reassignment of same value
Missing CHKERRQ(); Mostly in Tao code
Remove clang static analyser warning about passing NULL variable to strncat()
missing newline in -ts_monitor_extreme
minor fixes for integer counters
Configure: Deal with '__func__' in C89 builds with newer Clang and GCC.
Jenkinsfile: Increased timeout for tests to 5 minutes.
3.9 changes: further clarify removal of -pc_factor_mat_solver_package
Options deprecations: add "PETSc" to inline warning
removing unused variable
MatShift support added to MATSUBMAT. Mimics MATSHELL functionality. Needed for matrix-free Hessians in TAO Newton-Line-Search methods.
Add -ts_monitor_extreme
Dev manual: add note on deprecating options database keys
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Conflicts:
src/dm/impls/plex/examples/tests/ex4.c

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Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead

Merge branch 'master' into knepley/feature-snes-ex13-spectral

* master: (2350 commits)
migrate warning fix from next-tmp
Revert "Remove dead code."
clarifying comment in the code
Remove dead code.
Add JuMP citation
Copyedits and updates to developers manual
Add more protection to intrinsics
MPI: protect arguments in MPI macros
Add the missing conditionals for 64-bit build
Plex+VTK: Fix field type determination
Fix bug in name cleanup
Bib: Added ref
Plex+VTK: Fix field type determination
Plex: Updated test output - I am now hating this shit
forgot to save file after moving prototypes to petscsys.h
update Apple example project settings per Xcode
Two functions should actually be public, used, for example from Apple MacOS and iOS programs
includes should always be included relative to include directory
Apple removed old locations of docsets
SNES ex12: Updated test output
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Conflicts:
src/snes/examples/tutorials/ex13.c

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Merge branch 'barry/tao-to-new-test-harness' into barry/all-new-test-harness-branches

Merge branch 'jed/tests-cxx-linker' into barry/more-to-new-test-harness

Merge branch 'knepley/feature-plex-exodus-update'

* knepley/feature-plex-exodus-update: (22 commits)
this test requires exodus to be built with pnetcdf
Plex ex26: Fix leak and bad merge
Plex+E

Merge branch 'knepley/feature-plex-exodus-update'

* knepley/feature-plex-exodus-update: (22 commits)
this test requires exodus to be built with pnetcdf
Plex ex26: Fix leak and bad merge
Plex+ExodusII: Make all ExodusII calls into PetscStackCall
test: use newer cmake version for exodus
pnetcdf: correctly use flibs
exodus: update pnetcdf dependency - and make netcdf optional on pnetcdf And update exodus tests to use --download-pnetcdf
c89: fix
dmplex/exodus: fix build errors with exodus disabled
Plex: Guard ExodusII use
Plex ex26: Test 18 now working
Plex+ExodusII: Fixed hex27 bug
Plex ex26: Check in meshes
Plex ex26: Update to check ExodusII input and output
Plex+ExodusII: Added ExodusII viewer functions
Plex: For NtoG, we need to zero the output entries
Plex: After creating GtoN map, set useNatural for parallel DM
Plex: DMPlexVecRestoreClosure() now sets the input array to NULL
Plex+Doc: Improve documentation of Closure functions
BuildSystem: Bump ExodusII version
BuildSystem: added pnetcdf required for parallel access to non netcdf4/hdf5 exodus files
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Plex ex26: Check in meshes