DMPlex: Fix for C++ build, small fix for PetscFE

DMPlex: Removed leak from Triangle

DMPlex: Cleaned up some memory issues

DMPlex: Implement injection
- I don't think this should be required

DMPlex: DM interpolation requires the scaling vector for FAS

DMPlex: Fix DMPlexMatSetClosureRefined()
- Reject duplicate fine points
- Screen out point with dof = 0
- Fix the allocation for fine points

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTransp

Merge branch 'master' into knepley/feature-plex-fas

* master: (863 commits)
Revert "mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option."
MatCreateTranspose: fix for lazy block size
mpich: use latest mpich tarball with gcov but use '--enable-coverage' mpich configure option.
configure: add FC_DEFINE_FLAG to petscvariables
added a citation for pounders, Stefan finally came through
update to latest netcdf fixes bug that did not allow building on recent Mac OS X
DMPlex: Fixes for CGNS - Fixed loop bounds since CGNS uses closed intervals - Bug with mixed cell types - Typo with coordinates
final updates from nightly tests
fix for countcfunction
removed outdated docs and comments on MatStructure usage removed SAME_PRECONDITIONER since no longer used removed unneed use of MatStructure in Schur complement matrix
removed MatStructure arguments from Tao
fixes for Sundials and fun3d cannot use MPIU_SUM for integer arrays
inplace ILU factorization must update state of inplace matrix to prevent infinite recursion of updating PC
fixes for BDDC by the way not having BDDC always in the testing is going to lead to trouble
the compute Jacobian functions for SNES and TS now do not take a MatStructure flag
KSPSetOperators() no longer has the MatStructure argument. The Mat objects now track that information themselves. Use KPS/PCSetReusePreconditioner() to prevent the recomputation of the preconditioner if the operator changed in the way that SAME_PRECONDITIONER did with KSPSetOperators()
tracks when Mat's have a change in nonzero structure this information can be used by PC to determine how preconditioners must be rebuilt currently only does an error check if the user said same nonzero pattern but actually changed the pattern
completed cleanup of removal of matrix pointers to compute jacobian routines
makefile: Added 'make includegraph' to create an inclusion dependency graph.
Contrib: Updated include-graph.sh script to ignore *.hh files
...

Conflicts:
src/dm/dt/interface/dt.c

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DMPlex: Made a special MatSet for interpolation
- Maybe this can be generalized

DMPlex: Interpolation construction needs DM context

DMPlex: Allow DMCreateDefaultSection_Plex() to handle multiple fields

DMPlex: Diagnostic printing of matrices now allows rectangular input

DMPlex: Now DMPlexCheclSymmetry() also checks multiple cone/support entries

Merging master with feature-dmmoab. Only conflict was with SOURCECXX specification under impls/moab/makefile.

DMPlex: Added braindead simple parallel orientation solver
- This gathers the graph to proc 0, solves, and scatters the answer
- Need to store neighbor ranks and matches for each neighbor
- This shou

DMPlex: Added braindead simple parallel orientation solver
- This gathers the graph to proc 0, solves, and scatters the answer
- Need to store neighbor ranks and matches for each neighbor
- This should be replaced with a parallel BFS

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DMPlex: For 1D orientation, you have to use cone position rather than face orientation

Merged petsc/petsc into master

DMPlex: Correct error introduced when optimizing closure actions
- A single field may still have multiple components
- This error should have been detected by nightlies, but there is too much noise i

DMPlex: Correct error introduced when optimizing closure actions
- A single field may still have multiple components
- This error should have been detected by nightlies, but there is too much noise in the output now

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Merge branch 'master' into prbrune/snes-fascontinuation

Conflicts:
include/petscsnesfas.h

DM: Cast cleanup for DMGetField()

DM: If the local section is not present, it will be created automatically from PetscFE structures and boundary conditions
- Added createdefaultsection() to DM

DMPlex: Added DMBoundary struct
- This will replace the stuff in TS ex11

DMPlex: Adding support for interpolation between regularly refined meshes
- Added DMPlexComputeInterpolatorFEM()
- Added PetscFERefine()
- Added PetscFEIntegrateInterpolator_Basic()
- Not working now

DMPlex: Adding support for interpolation between regularly refined meshes
- Added DMPlexComputeInterpolatorFEM()
- Added PetscFERefine()
- Added PetscFEIntegrateInterpolator_Basic()
- Not working now since coarse meshes do not have Sections attached

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DMPlex: Fixed some small mistakes
- Initialize var
- Declare at the top of the block
- Added cone size call

Merge branch 'master' into barry/ts-rhsjacobian-only

Merge branch 'shri/update-SuiteSparse' into shri/external-package-KLU

Conflicts:
conf/test
config/examples/arch-linux-pkgs-dbg-ftn-interfaces.py
config/examples/arch-linux-pkgs-opt.py