DMPlex: Removed unused variables

DM: Added specialization for DMCreateSubDM() with a PetscSection
- Replace DMPlex implementation
- Is used by DMDA when a section is defined

DM: Added DMClone() which makes a shallow copy
- This is very useful for DM since it can have a lot of associated data and is used as a building block for different problems
- This replaces DMPlexClo

DM: Added DMClone() which makes a shallow copy
- This is very useful for DM since it can have a lot of associated data and is used as a building block for different problems
- This replaces DMPlexClone()

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DMPlex: Fixed bug in special case for DMPlexVecGetClosure()
- Need to set outgoing size if array is passed in

DMPlex: Added special case for DMPlexVecSetClosure()
- Could add more modes

DMPlex: Uniform refinement does not work on uninterpolated meshes

DMPlex: Optimizations for DMPlexVecGetClosure()
- Removed branch (seems to have little effect)
- Removed calculation of size when array is provided (profiled for 20% effect)

DMPlex: Fixed creation of global sections
- The size of neg[] must be all of nroots instead of pEnd-pStart

DMPlex: Optimize depth retrieval by storing a pointer to the label
- This is a little unsafe since someone could go in and create a new "depth" label out from under you

DMPlex: DMGetSubDM_Plex() had a memory leak
- It was also doing extra work

DMPlex: Allow DMPlexVecGetClosure() to take an input array

DMPlex: Fix bug in specialization of DMPlexVecGetClosure()

DMPlex: Bug fix for special case in DMPlexVecGetClosure()

DMPlex: Added optimization for depth 1 DMPlexVecGetClosure()

Merged petsc/petsc into rmills/petsc master.

DMPlex: Better fix for distribution of hybrid bounds
- Bounds are now computed from the reordering at distribution time
- Still incomplete since we need to compute the interpolated bounds after inter

DMPlex: Better fix for distribution of hybrid bounds
- Bounds are now computed from the reordering at distribution time
- Still incomplete since we need to compute the interpolated bounds after interpolation

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DMPlex: Temporary fix for handling hybrid meshes in parallel
- Try to compute the hybrid structure
- Should really send it out with Distribute()

DMPlex: Allow DMPlexOrient() of empty mesh

DMPlex: Move Mat option set after preallocation
- SEGV on SBAIJ if we do not do this

DMPlex: Do not allow default sections in DMPlexMatSetClosure()
- This makes the call collective

DMPlex: Added generic DMPlexInvertCell() to aid in changing orientation to the internal convention

DMPlex: Added ex9 to test performance, put in depth 1 special case for TransitiveClosure

DMPlex: Fixed bug with mesh orientation
- flipped marker must be a boolean for ^ operation
- Final check needs a mismatch as well

Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: Fixed bug in DMPlexOrient() - Must visit faces in BFS order so that all comparisons are in a connected component of the mesh
DM: Fix leak

Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: Fixed bug in DMPlexOrient() - Must visit faces in BFS order so that all comparisons are in a connected component of the mesh
DM: Fix leak when creating global section
DMPlex: Fix allocation for embedded submesh
DMPlex: Removed debugging prints
DMPlex: Fix leak in interpolation
DMPlex: Added DMPlexOrient() which correctly orients a set of adjacent cells - You need this when extracting an embedded submesh
DMPlex: Fix memory management in submesh creation

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DMPlex: Fixed bug in DMPlexOrient()
- Must visit faces in BFS order so that all comparisons are in a connected component of the mesh