Plex: Fix overlap point SF generation

Plex: Build complete overlap label and stratify resulting SF.

Instead of building an SF of overlap contributions and merging it with
locally owned points, we now build a label of overlap and owned p

Plex: Build complete overlap label and stratify resulting SF.

Instead of building an SF of overlap contributions and merging it with
locally owned points, we now build a label of overlap and owned points
and stratify the resulting SF via a new utility function.

Note: This changes the point numbering of overlapping plexes, and thus
requires a test update for ex12.

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Plex: No longer require the "marker" label for generation or refinement

Plex: Create parallel partitions that ParMetis accepts

For this we need to convert the cell graph into (positive) global numbers
and drop all overlap cells.

Plex: Derive original point numbering in DMPlexMigrate

We now don't need to carry around ISLToGs in DMPlexDistribute(Overlap).

Plex: Move DM migration into subroutine that deals with point numberings

DMPlexMigrate can optionally back out any previous local numbering or
assume a zero-to-all-ranks pattern to derive the new lo

Plex: Move DM migration into subroutine that deals with point numberings

DMPlexMigrate can optionally back out any previous local numbering or
assume a zero-to-all-ranks pattern to derive the new local numbering.

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Plex: Bug fix in DMPlexDistribute; only kill the migration SF once

Plex: Re-implement routine to create partitioner graph

Plex: Enable n-level overlap in DMPlexDistribute

Adds a utility function DMPlexPartitionLabelAdjacency, which adds a full
level of adjacency to the partitioning label.

Plex ex12: Add tests for 2-level overlap and redistribute/load balancing

Load balancing is performed by prescribing a disjoint partitioning
and calling a second DMPlexDistribute step with parmetis.

Plex ex12: Add tests for 2-level overlap and redistribute/load balancing

Load balancing is performed by prescribing a disjoint partitioning
and calling a second DMPlexDistribute step with parmetis.

Also, remote ParallelOverlap from ex12.c, since all this is now tested
implicitly via DMPlexDistribute.

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Plex: Fix for cohesive labeling
- We now allow two cohesive patches to touch directly
- This seems to allow hybrid cells to be in the star of fault vertices for other faults, but we have not reproduc

Plex: Fix for cohesive labeling
- We now allow two cohesive patches to touch directly
- This seems to allow hybrid cells to be in the star of fault vertices for other faults, but we have not reproduced this on a small enough example to check
- I just filter out hybrid points when labeling

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Plex: Switch initial distribution to using partition labels

After creating a cell partition we now convert this into a label and
reuse the same utility routines to add the closure and transform the

Plex: Switch initial distribution to using partition labels

After creating a cell partition we now convert this into a label and
reuse the same utility routines to add the closure and transform the
label into a migration SF.

Note: Obsoletes PetscSFConvertPartition and DMPlexCreatePartitionClosure

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Merge branch 'knepley/fix-plex-examples-refinement'

* knepley/fix-plex-examples-refinement:
Plex ex12: Add test output
Plex: Restore Fortran binding for DMPlexDistribute()
SNES ex12: Fix SetFr

Merge branch 'knepley/fix-plex-examples-refinement'

* knepley/fix-plex-examples-refinement:
Plex ex12: Add test output
Plex: Restore Fortran binding for DMPlexDistribute()
SNES ex12: Fix SetFromOptions usage
SNES ex12: Fix refinement usage

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Merge remote-tracking branch 'lawrence/petscpartitioner-doc'

* lawrence/petscpartitioner-doc:
Fix docstring of PetscPartitionerShellSetPartition

Merge remote-tracking branch 'lawrence/petscpartitioner-set'

* lawrence/petscpartitioner-set:
Note refcounting in DMPlexGetPartitioner
Add programmatic interface to set partitioner on DMPlex

Merge branch 'knepley/fix-plex-tetgen'

* knepley/fix-plex-tetgen:
Plex: Fix for TetGen wrapper

Plex: Add DMPlexPartitionLabelClosure

Adds the closure of all points to the partition label.

Plex: Add DMPlexPartitionLabelInvert utility routine

Given a label describing a send pattern, this routine creates the
according receive pattern from which we can build the SF.

Plex: Add DMPlexPartitionLabelCreateSF utitlity routine

This routine creates an SF from a DMlabel assigning ranks
to remote root numbers.

Plex ex12: Adding test partitions and enabling full partitioning tests

We now test the full partitioning of a 2x2 square on 3 and 8 ranks
with and without overlap via .tex output.

Plex ex1: Adding sample output for 8 rank parallel refinement test

Plex: Ensure refined label is created with same number of strata

This fixes a corner case where empty label strata cause failures during
parallel refinement. Thanks to Lawrence Mitchell for providin

Plex: Ensure refined label is created with same number of strata

This fixes a corner case where empty label strata cause failures during
parallel refinement. Thanks to Lawrence Mitchell for providing this patch.

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Plex ex1: Add fixed test partitions and test on 8 ranks

This captures a corner case failure during parallel
refinement due to empty label strata.

Plex ex1: Add test for overlap creation after parallel refinement

Perform refinement in parallel and add overlap region on the fine mesh.

Merge branch 'barry/fix-options-default'

Conflicts:
src/ksp/ksp/examples/tutorials/ex52.c