DMPlex: Major overhaul of hybrid meshing
- Put it hybrid faces and supports for hybrid edges
- Cleaned up calculation of new point numbering

DMPlex ex5: Hybrid bounds are now calculated by DMPlexDistribute()

DMPlex ex5: Better documentation on tests

DMPlex: Simplify the calculation of sizes in hybrid cell creation

DMPlex ex4: Better handling of DM

DMPlex: Added DMPlexCheckSymmetry() and DMPlexCheckSkeleton()
- These are diagnostic functions

DMPlex ex5: Fixed leak, removed DM from context, added output for last test

Merge branch 'knepley/feature-closure-cache'

* knepley/feature-closure-cache:
DMPlex: Added declaration of DMPlexCreateClosureIndex()
SNES ex62: Use closure index
DMPlex: Use closure index if

Merge branch 'knepley/feature-closure-cache'

* knepley/feature-closure-cache:
DMPlex: Added declaration of DMPlexCreateClosureIndex()
SNES ex62: Use closure index
DMPlex: Use closure index if available for DMPlexVecGetClosure()
DMPlex: Added DMPlexCreateClosureIndex() - Uses a PetscSection+IS and stashes in the original Section
PetscSection: Added an index for optimization of closure queries - Added PetscSectionGet/SetClosureIndex() - The index is keyed to the DM which built it (use PetscObject) - Only use a single key for now since a lot of checking would be slow

Conflicts:
src/snes/examples/tutorials/ex62.c

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Merge branch 'knepley/feature-plex-generic-distribute'

* knepley/feature-plex-generic-distribute:
mpiuni: add in MPI_Type_f2c()
DMPlex: add missing declarations DMPlexDistribute{Field,Data}
bf

Merge branch 'knepley/feature-plex-generic-distribute'

* knepley/feature-plex-generic-distribute:
mpiuni: add in MPI_Type_f2c()
DMPlex: add missing declarations DMPlexDistribute{Field,Data}
bfort: update to using MPI_Type_f2c() [for plexf.c]
DMPlex: Added DMPlexDistributeData() to distribute arbitrary data types
DMPlex: Change DMPlexDistribute() to give back the PetscSF - This can be used to distribute sections and fields

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DMPlex: Put in size for hybrid tet uniform refinement

DMPlex: Output hybrid structure in view

DMPlex: Fix leak in 3d refinement

DMPlex ex4: Added new tet hybrid test, and check symmetry of all meshes
- Allow viewing of initial mesh

DMPlex ex4: Correct static array size

DMPlex: Fixed misuse of PetscObjectSetName()

Merge branch 'knepley/feature-plex-generic-distribute' into knepley/feature-plex-reordering

The DMPlexDistribute interface changed to return a PetscSF.

* knepley/feature-plex-generic-distribute:

Merge branch 'knepley/feature-plex-generic-distribute' into knepley/feature-plex-reordering

The DMPlexDistribute interface changed to return a PetscSF.

* knepley/feature-plex-generic-distribute:
mpiuni: add in MPI_Type_f2c()
DMPlex: add missing declarations DMPlexDistribute{Field,Data}
bfort: update to using MPI_Type_f2c() [for plexf.c]
DMPlex: Added DMPlexDistributeData() to distribute arbitrary data types
DMPlex: Change DMPlexDistribute() to give back the PetscSF - This can be used to distribute sections and fields

Conflicts:
include/petscdmplex.h

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Mat: Changed MatCalcBandwidth() to MatComputeBandwidth()
- Added Fortran interface

DMPlex ex10: This tests reordering of meshes

DMPlex: Added DMPlexGetOrdering() and DMPlexPermute()

DMLabel: Added DMLabelPermute()

DMPlex: Added DMPlexCreateDoublet()

DMPlex: Added DMPlexCopyLabels()

Merge branch 'knepley/fix-plex-ex12'

* knepley/fix-plex-ex12:
DMPlex ex12: Give mesh a name - Fixed test output
DMPlex: Fix leaks

Merge branch 'barry/dmvecmattypes'

The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.

* barry/dmvecm

Merge branch 'barry/dmvecmattypes'

The MatType argument is removed from DMCreateMatrix(), you can use
DMSetMatType() to indicate the type you want used with a DM, defaults to
MATAIJ.

* barry/dmvecmattypes:
DMPlex ExodusII: fix dm->vectype pointer syntax
removed use of VecSetFromOptions() all over the placed, instead use MatGetVecs() or use dm->vectype to determine type added DMGetVecType() and DMGetMatTYpe()
removed MatType argument from DMCreateMatrix() and DMCreateColoring() since information is obtained from DM

Conflicts:
src/dm/impls/da/fdda.c
src/dm/impls/plex/plex.c

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Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-d

Merge branch 'jed/remove-dynamic-loading-option'

Option --with-dynamic-loading has been removed. Similar functionality
is available via the run-time option -dynamic_library_preload.

* jed/remove-dynamic-loading-option:
Sys: PetscContainerCreate must call PetscSysInitializePackage
Remove --with-dynamic-loading / PETSC_USE_DYNAMIC_LIBRARIES

Conflicts:
src/dm/impls/mesh/mesh.c
src/dm/interface/dlregisdmdm.c
src/docs/website/documentation/changes/dev.html

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