PetscDS: add missing PetscDSCopyBoundary, fix copy loops

DM: set PetscDS from options in DMSetFromOptions()

DM, PetscDS: remove redundant boundary representations

The DMBoundary is now just a container for the DSBoundary

Plex: Fixed bad assumption of sorted Label values

IS+Plex: Changed interface to closure permutation to take an IS

Plex ex9: Can now test closure reordering
- Also fixed some small bugs

Plex ex6: Example that shows how to set and retrieve values with the spectral element ordering

Plex: Allow closure permutation in PlexVecGet/SetClosure()
- This supports spectral element ordering
- This does not seem to introduce any performance degradation

Plex: Added DMPlexCreateSpectralClosurePermutation()

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize t

Merge branch 'tisaac/ts-ex11-amr'

We now have an example (ts/examples/tutorials/ex11.c) where we can
use either DMPlex or DMP4est to handle adaptivity when time stepping.
We have tried to minimize the amount of code that is specialized to the
different DMs, and in the future more work can be done to improve this
interface.

* tisaac/ts-ex11-amr: (62 commits)
DMP4est: type fix
Plex: Fixes for analyzer
DMP4est: update snes ex12 regressions
DMPlex: fix parent/child interpolation with numFields > 0
DMP4est: also compute anyChange for uniformly refined/coarsened meshes
TS ex11: fix command line for AMR without computed gradients
TS ex11: remove gradient reconstruction from adaptivity requirements
DMPlexTree: some compilers want this var initialized
Plex: Changed Get/RestoreFaceFields() and Get/RestoreFaceGeometry() to return the number of active faces - This fixes a long-standing bad access in FV, although the values were never actually used.
DMPlexTS: removed unused variables
DMPlex/DMP4est: small fixes for next warnings and errors
SNES ex36 and ex52: These do not work anymore
DMPforestGetTransferSF_Point(): try to match parents
PetscViewerHDF5: destroy old file data if setting new filename
DMPlex + FV: remove leaky references in projection functions
Plex: Fixed incredibly stupid bug in Jacobian computation
PetscViewer HDF5: added get name method
DMPlexTree: do not skip out of child matrix loops early
PetscFV: correct field offsets when limiting gradients
DMP4estTree: ignore negative values when getting/setting vector values for transfer
...

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DMPLEX: disable generation of fortran stub for DMPlexGetSubdomainSection

DMPlex: fix parent/child interpolation with numFields > 0

There were several instances of off-by-one errors that had not been tested before but are tested now

Plex: Since we are using an SF, ranks that are not found default to 0, not -1
- You need to check the index for the negative value

Plex: Added a new point location type to remove entries which are not found
- This was the default, but its not what DMSwarm wanted and its non-intuitive I agree

DMPlex: construct the correct l2gmap for MatIS using the subdomainSection (for local indexing) and the globalSection

Update ComputeJacobian to set the closure in the local matrix

Plex: Added PetscDraw support

Plex: If point not found, return DMLOCATEPOINT_POINT_NOT_FOUND

Plex: Doc fix

DMPLEX: filling the matrix during preallocation will generate MAT_NEW_NONZERO_ALLOCATION_ERR (on the local matrices) with MATIS

In order to be set up properly, MATIS needs to know the l2gmap before any preallocation

The communicator for the l2gmap provided by the DM should be the same of the DM

Merge branch 'dmay/feature-dm-swarm' into knepley/feature-plex-particle-example

* dmay/feature-dm-swarm: (69 commits)
DMSwarm: * Check for size compatabaility between vectors created for DMSwarm f

Merge branch 'dmay/feature-dm-swarm' into knepley/feature-plex-particle-example

* dmay/feature-dm-swarm: (69 commits)
DMSwarm: * Check for size compatabaility between vectors created for DMSwarm fields * Bug fix for the field register function
DMSwarm DataBucket: * Added guards to ensure that internal arrays are never re-sized if any raw pointers are being currently being accessed
DMSwarm: * Added missing part of macro
DMSwarm: * Added documentation
DMSwarm example: * Added example with DMShell and user point location
DMSwarm Migrate: * Updated to use DMLOCATEPOINT_POINT_NOT_FOUND flag
DM definition: * Added special flag for marking points as being not found within an element during a call to DMLocatePoints
DMSwarm migrate: * Fixed bug with point removal
DMSwarm: * Removed print from data exchanger
DMSwarm: * Use common field names * Re-organized init/finalize fields with DMCreate/DMSetUp * Added methods, flags, checks when using DMSwarmType PIC
SwarmMigrate: * Use common field names
PetscDMSwarm: * Added common names * Corrected extern to PETSC_EXTERN * Added names for migrate
DMSwarm implementation: * Remove unused member
DM implementation: * Added new method locatepointssubdomin
DataBucket: * Print block size
DMSwarm example: * Removed comment
DMSwarm example: * Updated function names
DMSwarm test: * Added new test for variable block sizes
DMSwarm: * Fixed typo in vector name
DMSwarm: * Finishing support for block size != 1
...

Conflicts:
include/petsc/private/dmimpl.h

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Plex: Expose projection routines

Merge branch 'knepley/feature-dm-point-location-failure'

* knepley/feature-dm-point-location-failure:
Plex: Fixed declaration and complex conversion
DM: Added mode to DMLocatePoints() to change

Merge branch 'knepley/feature-dm-point-location-failure'

* knepley/feature-dm-point-location-failure:
Plex: Fixed declaration and complex conversion
DM: Added mode to DMLocatePoints() to change failure behavior - Implement to NEAREST mode in Plex for 2D simplices - Added DMPlexCLosestPoint_Internal()

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DMPlexTree: some compilers want this var initialized

DMPlex/DMP4est: small fixes for next warnings and errors