DMPlex: uses BCs, FV gradient reconstruction in DMPlexTransferVecTree()

The reason these can be in the tranfer function but not in the tranfer
matrix constructors (interpolate or inject) is that the

DMPlex: uses BCs, FV gradient reconstruction in DMPlexTransferVecTree()

The reason these can be in the tranfer function but not in the tranfer
matrix constructors (interpolate or inject) is that these are nonlinear
(either affine from boundary conditions or whatever from gradient
limiting)

WIP: reconstruct gradients when interpolating

Plex: introduce gradient reconstruction into DMPlexTransferVecTree

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DMPlex: move FV methods out of DMPlexSNES and into their own file

DMPlex: cache FVM data

Merge branch 'pr478/knepley/feature-dmplex-adapt/master'

* pr478/knepley/feature-dmplex-adapt/master: (34 commits)
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GM

Merge branch 'pr478/knepley/feature-dmplex-adapt/master'

* pr478/knepley/feature-dmplex-adapt/master: (34 commits)
SNES ex12: Fixed unstructured GMG test
SNES ex12: Added another unstructured GMG test
petsc4py: use the snapshot with the fix for dmplex change
Plex ex19: Added DMSetFromOptions()
Plex: Store a flag indicating whether the boundary should change during remeshing - Set using -dm_plex_remesh_bd - Changed Remesh_Internal() signature
Always coarsen boundaries.
Plex: Fixed option name
Plex: Protect unused variables
Plex: Fixes for c89
Plex: Fixes for complex
SNES ex12: Updated output for coarsening
Plex ex3: Updated output for coarsening
Plex ex19: Now working with refactored Adapt()
Plex: Refactored DMPlexAdapt() - Added DMPlexRemesh_Internal() - Use Remesh inside DMCoarsen_Plex() - Use Join() to set label on faces
Plex ex19: Simplified parallel construction of metric
Plex ex19: General cleanup
Plex: DMPlexCreateBoxMesh() now takes the number of faces
Add output files for tests
Fix previous memory fix
Fix memory problems
...

Conflicts:
config/BuildSystem/config/packages/petsc4py.py
config/builder.py

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Merge branch 'knepley/feature-parallel-mesh-load'

* knepley/feature-parallel-mesh-load:
Plex ex18: Small fixes - Use DMBOUNDARY_NONE correctly, document partition edges
Plex ex18: Added simplex

Merge branch 'knepley/feature-parallel-mesh-load'

* knepley/feature-parallel-mesh-load:
Plex ex18: Small fixes - Use DMBOUNDARY_NONE correctly, document partition edges
Plex ex18: Added simplex 3D tests
fix compile warnings
Plex: Removed unused variable
DMLabel: Fixed DMLabelGather() - The leaves are not compact, but rather follow the local numbering, so we need to allocate nroots space
Plex: Fix for parallel interpolation
Plex-ex18: Enabling 2D simplex tests with interpolation
Plex: Create pointSF for edge/facet points after interpolation
Plex-ex18: Add another test for 2D simplices on 3 ranks
Plex: Fix hash usage in DMPlexBuildFromCellList_Parallel_Private
Plex ex18: Added test for parallel mesh loads - Interpolation test is broken
Plex: Fixed static declaration of some functions
Plex: Added DMPlexCreateFromCellListParallel() - This directly creates a parallel mesh from pieces

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Plex: Remove unused variables

Plex: Updated examples to new DMPlexCreateBoxMesh()

Plex ex19: Added DMSetFromOptions()

Plex: Store a flag indicating whether the boundary should change during remeshing
- Set using -dm_plex_remesh_bd
- Changed Remesh_Internal() signature

Always coarsen boundaries.

Plex: Fixed option name

Plex: Protect unused variables

Plex: Fixes for c89

Plex: Fixes for complex

Plex ex3: Updated output for coarsening

Plex ex19: Now working with refactored Adapt()

Plex: Refactored DMPlexAdapt()
- Added DMPlexRemesh_Internal()
- Use Remesh inside DMCoarsen_Plex()
- Use Join() to set label on faces

Plex ex19: Simplified parallel construction of metric

Plex ex19: General cleanup

Plex: DMPlexCreateBoxMesh() now takes the number of faces

Plex: Fixed ComputeIntegral() to work with FVM
- May still have a bug, not sure

plexgmsh: Read Cell Sets as well as Face Sets

Add output files for tests

DMPlexTree: use local vector to interpolate in transfer

Plex: added labels on all processes