TS ex11+DMPlex: Treat ghost cells as hybrid cells

DMPlex: Changing meaning of boundary label in DMPlexLabelCohesiveComplete()
- Now it marks vertices already present in the original label
- We mark these as unsplit, and ignore their stars
- Remove o

DMPlex: Changing meaning of boundary label in DMPlexLabelCohesiveComplete()
- Now it marks vertices already present in the original label
- We mark these as unsplit, and ignore their stars
- Remove old code

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DMPlex: Fixed stupid typo

DMPlex: Fixed refinement to respect embedded manifolds

DMPlex: Fixed types in DMPlexOrient()

DMPlex: Fixed initialization in DMPlexLabelCohesiveComplete()

PetscFV: Initial checkin
- Added an Upwind implementation

Merge branch 'knepley/feature-plex-hdf5-parallel-load'

* knepley/feature-plex-hdf5-parallel-load:
HDF5: Fixed Xdmf script
Plex+HDF5: Do not use vectors for periodic visualization
Plex+HDF5: Ig

Merge branch 'knepley/feature-plex-hdf5-parallel-load'

* knepley/feature-plex-hdf5-parallel-load:
HDF5: Fixed Xdmf script
Plex+HDF5: Do not use vectors for periodic visualization
Plex+HDF5: Ignore negative sequence numbers
DMPlex: Now Plex output is parallel - We now write visualization specific topology in /viz/topology - We output a point reordering, coneSizes, cones, and orientations - Now longer need to interpolate on load
DMPlex: Use the presence of faceGeometry in the DM to signal we are using FVM - This will become a PetscFVM object soon
DMPlex: Preserve the block size of the coordinate vector after distribution
Plex+HDF5: Moved all HDF5 to a separate file, and mapped 2D periodic mesh to the cylinder - Now visualization specific things are in /viz
HDF5: Made petsc_gen_xdmf.py executable
Viewer+Options: Added Fortran interface for PetscObjectViewFromOptions()
IS: Stupid mistake. Damn you compiler
DMPlex: Now parallel HDF5 label output does not fail - However, it is also now clear that we will have to write the full interpolation connectivity in order for these to be meaningful
DMPlex: Added DMPlexCreatePointNumbering() - Made DMPlexCreateNumbering_Private() more flexible
IS: Added ISSortRemoveDups()
DMPlex: Added DMPlexInvertCell_Internal() - Stupid type matching
HDF5: Added petsc_gen_xdmf.py which processes PETSc HDF5 output and produces an Xdmf file
DMPlex: Force a serial load in DMLoad_HDF5(), after which we call DMPlexDistribute() - Eventually we would load into a naive partition
IS+HDF5: Corrected code for new block size interface where it is never negative
Viewer+HDF5: Added PetscViewerHDF5ReadSizes() - This allows me to check the size of a Vec or IS to be loaded

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DMPlex: Fixed logic in hybrid cell tagging and added missing declaration

DMPlex Fixed huge error with last change set
- Default cellHeight is 0

DMPlex: Allow cellHeight argument for DMPlexMarkBoundaryFaces()

DMPlex ex3: Added tests for P1disc

PetscFE: Added domain integration
- Added PetscFEIntegrate(), only implemented for Basic
- Added DMPlexComputeIntegralFEM() and DMPlexComputeL2FieldDiff()
- This should replace the L2Diff functions

DMPlex: Added blabel argument to DMPlexLabelCohesiveComplete()
- Lets user designate the boundary of a dividing surface
- Added GetSurfaceSize_Static()

DMPlex: Fix for DMPlexOrient()
- I was not symmetrizing the orientation graph on processes

DMPlex: Added DMPlexAddConeSize()

DMPlex: Fixed memory overwrite at depth 0 for viewing

DMPlex ex3: Updated for corrected cell dof

DMPlex ex3: Added test case for P1disc on a quad

DMPlex ex3: Added P1 discontinuous test
- Something looks wrong with interpolation

DMPlex ex3: Switched transcendental function to tanh()
- Put in flag for convergence rate test, only do it once for each element

DMPlex ex3: Put in a test for convergence rates
- The weird convergence rates in 3D come from the irregular shapes of the original cells, so
that the longest edge is not actually decreasing by a f

DMPlex ex3: Put in a test for convergence rates
- The weird convergence rates in 3D come from the irregular shapes of the original cells, so
that the longest edge is not actually decreasing by a factor 2
- Something is wrong with the Q convergence rates

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DMPlex: Do not automatically turn off uniform refinement

DMPlex+Doc: Fixed function doc
Reported-by: Brad Aagaard <baagaard@usgs.ggov>

Merge branch 'knepley/feature-optcontrol-mg' into knepley/feature-fe-dg-space

* knepley/feature-optcontrol-mg:
TAO ex1: documentation
TAO ex1: Now we have a full optimal control problem - The da

Merge branch 'knepley/feature-optcontrol-mg' into knepley/feature-fe-dg-space

* knepley/feature-optcontrol-mg:
TAO ex1: documentation
TAO ex1: Now we have a full optimal control problem - The data for the state is perfect (Q is I) - The regularization is perfect (L is I and a_ref is the exact control)
TAO ex1: Constructed saddle point problem, but control is given exactly
PetscFE: Fix array initialization bug
TAO ex1: Starting an IPM example
DMPlex: When creating a section, we should only complete a label once
DMPlex: Now DMPlexProjectFieldLocal() correctly masks out fields with no function
DMPlex: Added DMPlexVecSetFieldClosure_Internal() - Allows fields to be masked
SNES ex62: Updates for printing changes
DMPlex: Fixes preallocation checks
SNES ex12: Updates for printing changes

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