DM: Eliminate DMPlexGet/SetAdjacencyUseCone/Closure() in favor of DMGet/SetBasicAdjacency()

DM+DS: Move adjacency from DS to DM
- Added DMGet/SetAdjacency()
- Altered DMView when fields are set
- Copy default adj on Clone, and field adj on CopyFields

Merge branch 'knepley/fix-ds-init' [PR #1415]

* knepley/fix-ds-init:
DM: Fix DS initialization, so that we can setup the discretization multiple times

Revert "Merge branch 'knepley/fix-ds-init' [PR #1415]"

This reverts commit 37bb5b94b6914f9a726e34e5bf9c9c8b40dda9f0, reversing
changes made to 4a21182031185fd5d7353432f9213cf374069ae2.

The reason f

Revert "Merge branch 'knepley/fix-ds-init' [PR #1415]"

This reverts commit 37bb5b94b6914f9a726e34e5bf9c9c8b40dda9f0, reversing
changes made to 4a21182031185fd5d7353432f9213cf374069ae2.

The reason for this revert is an incorrect merge of a local copy of knepley/fix-ds-init.

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Merge branch 'knepley/fix-ds-init' [PR #1415]

* knepley/fix-ds-init:
Fix DS initialization, so that we can setup the discretization multiple times

Merge branch 'knepley/feature-partitioner-viewer' [PR #1411]

* knepley/feature-partitioner-viewer:
PetscPartitioner: Added viewer for partition graph

Plex: Added DMPlexGetAuxiliaryPoint(), and used it in integration
- It was already being used in projection

Plex: Change slightly the check for higher order coordinates

Plex: Copy discretization when creating coordinate DM

DM: Setup DS for coordinate DM

Plex ex10: Forgot to create DS

Plex: Reordering should preserve the discretization

DM: Fix DS initialization, so that we can setup the discretization multiple times
- Clear out DS when changing DM fields
- Do not error if we cannot find a DS, just return NULL
- If there is no defau

DM: Fix DS initialization, so that we can setup the discretization multiple times
- Clear out DS when changing DM fields
- Do not error if we cannot find a DS, just return NULL
- If there is no default DS, make one in DMCreateDS()
- When checking for a DS in the coordinateDM, allow NULL

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Plex: Change slightly the check for higher order coordinates

Plex: Copy discretization when creating coordinate DM

DM: Setup DS for coordinate DM

Merge branch 'knepley/fix-dm-setfields' into knepley/fix-ds-init

* knepley/fix-dm-setfields:
Plex ex10: Forgot to create DS
Plex: Reordering should preserve the discretization

Plex ex10: Forgot to create DS

Plex: Reordering should preserve the discretization

DM: Fix DS initialization, so that we can setup the discretization multiple times
- Clear out DS when changing DM fields
- Do not error if we cannot find a DS, just return NULL
- If there is no defau

DM: Fix DS initialization, so that we can setup the discretization multiple times
- Clear out DS when changing DM fields
- Do not error if we cannot find a DS, just return NULL
- If there is no default DS, make one in DMCreateDS()
- When checking for a DS in the coordinateDM, allow NULL

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PetscPartitioner: Added viewer for partition graph

DMPlex: Fix bogus compiler warnings in Gmsh reader

DMPlex: Fix reader for Gmsh v4 format

- Entities are not numbered contiguously

Merge branch 'hzhang/dmplex/ex18-add-1d' [PR #1379]

* hzhang/dmplex/ex18-add-1d:
add 1D test case to src/dm/impls/plex/examples/tests/ex18.c for understanding DMNetwork
enable runtime options ncells

Merge branch 'hzhang/dmplex/ex18-add-1d' [PR #1379]

* hzhang/dmplex/ex18-add-1d:
add 1D test case to src/dm/impls/plex/examples/tests/ex18.c for understanding DMNetwork
enable runtime options ncells > 3; parmetis re-distributes for np=2

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Doc: Added seealso for pair of functions