Merge branch 'barry/2022-05-03/cleanup-makefiles' into 'main'

remove unneeded stuff from makefiles

See merge request petsc/petsc!5211

remove garbage from makefiles

Including
* unused FLAGS variables
* All: lib that did not work
* stray blank lines etc

Commit-type: housekeeping
/spend 1h

Merge branch 'knepley/feature-plex-parallel-submesh' into 'main'

Adding parallel handling of extracted submanifolds

See merge request petsc/petsc!5101

Plex: Factor out point queue structure
- Added DMPlexPointQueue and API
- Updated SBR refinement
- Fixed small bug with DMLabelPropagatPush() in serial

Merge branch 'jwallwork23/mmg-trim' into 'main'

Plex interface for Mmg and ParMmg

See merge request petsc/petsc!4431

plex adapt: finish integration of Mmg and ParMmg

Note that the interfaces for Pragmatic, Mmg
and ParMmg now exist in their own subdirectories

DM: Take over management of mesh generators and adaptors from DMPlex
- Change adaptLabel signature to match adaptMetric
- Move mesh generator list from DMPlex to DM
- DMAdaptLabel() and DMAdaptMetric

DM: Take over management of mesh generators and adaptors from DMPlex
- Change adaptLabel signature to match adaptMetric
- Move mesh generator list from DMPlex to DM
- DMAdaptLabel() and DMAdaptMetric() now check this list
- Register metric adaptation packages
- Change -dm_plex_generator to -dm_generator
- Change -dm_plex_adaptor to -dm_adaptor

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Merge branch 'knepley/feature-plex-extrude-symmetric' into 'main'

Plex: DMPlexExtrude() can now symmetrically extrude

See merge request petsc/petsc!4367

DM: Now extrusion is like DMRefine() and implemented through DMPlexTransform - DMExtrude() replaces DMPlexExtrude() - Added an extrusion transformation - Added DMPlexTransformSetDimensions() and setd

DM: Now extrusion is like DMRefine() and implemented through DMPlexTransform - DMExtrude() replaces DMPlexExtrude() - Added an extrusion transformation - Added DMPlexTransformSetDimensions() and setdimensions function - DMPlexTransformMapCoordinates() and DMPlexSnapToGeomModel() now take the coordinate dimension - -dm_extrude replaces -dm_plex_extrude_layers

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Merge branch 'jwallwork23/metric-utils' into 'main'

Plex metric utils

See merge request petsc/petsc!4337

plex metric: utilities for Riemannian metric

Merge branch 'knepley/feature-orientation-rethink' into 'main'

Plex: Rethink Plex orientation

See merge request petsc/petsc!4218

Plex: DMPlexTransform is now the way to manipulate a Plex
- Replace DMPlexCellRefiner with DMPlexTransform
- Replace CellRefinerInCellTest_Internal() with DMPolytopeInCellTest()
- Replace DMPlexCe

Plex: DMPlexTransform is now the way to manipulate a Plex
- Replace DMPlexCellRefiner with DMPlexTransform
- Replace CellRefinerInCellTest_Internal() with DMPolytopeInCellTest()
- Replace DMPlexCellRefinerGetAffineTransforms() with
DMPlexRefineRegularGetAffineTransforms()

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Merge branch 'knepley/feature-opencascade' into 'main'

Plex: Separated EGADS and EGadsLite functionality, many fixes

See merge request petsc/petsc!3870

Plex: Separated EGADS and EGadsLite functionality, many fixes
- Added DMPlexCreateEGADSLiteFromFile()
- Added DMPlexInflateToGeomModel()
- Added test CAD meshes
- Fixed bug in CTetGen labeling
- Fixe

Plex: Separated EGADS and EGadsLite functionality, many fixes
- Added DMPlexCreateEGADSLiteFromFile()
- Added DMPlexInflateToGeomModel()
- Added test CAD meshes
- Fixed bug in CTetGen labeling
- Fixed memory leak in TetGen
- Added support for -dm_plex_view_labels in ASCII viewer
- Added -dm_plex_ignore_model to disable snap-to-CAD for refinement

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Merge branch 'knepley/feature-plex-ceed-integration' into 'main'

Plex: Initial CEED integration

See merge request petsc/petsc!3918

DM+Plex+FE: Initial CEED integration
- Plex ex42: Surface area CEED example

Merge branch 'dalcinl/partitioner' into 'master'

PetscPartitioner: Reorganize code in a proper package subtree

See merge request petsc/petsc!2941

PetscPartitioner: Reorganize code in a proper package subtree

Merge remote-tracking branch 'origin/maint'

Merge remote-tracking branch 'origin/jolivet/fix-symlink-free' into maint

Single petscdir.mk

Merge remote-tracking branch 'origin/more-updates-for-missing-petsc_dir'

More support for not needing to set PETSC_DIR yet build with PETSc, also...

See merge request petsc/petsc!2626

build: add more support for not needing to set PETSC_DIR yet build with PETSc, also support for GNU make to directly use "make test" instead of "make -f gmakefile.test"

Still needs -include ../petsc

build: add more support for not needing to set PETSC_DIR yet build with PETSc, also support for GNU make to directly use "make test" instead of "make -f gmakefile.test"

Still needs -include ../petscdir.mk in many of the makefiles
Still needs the link for ../petscdir.mk in many directories

GNUMakefile: call legacy makefile recursively instead of including it

GNUMakefile: promote default "all" target; "libs" builds libpetsc*

GNUMakefile: If gnumake < 4.2 prefer makefile wrapper interface over direct gmakefile interface to avoid the following warnings

gmakefile.test:92: arch-ci-linux-cxx-cmplx-pkgs-64idx/tests/testfiles: No such file or directory
gmakefile:67: arch-ci-linux-cxx-cmplx-pkgs-64idx/lib/petsc/conf/files: No such file or directory

Commit-type: testing-fix, feature, usability
Thanks-to: Jed Brown jed@jedbrown.org

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Merge branch 'jed/promote-examples-tests-tutorials' [petsc/petsc!2610]

* jed/promote-examples-tests-tutorials:
Promote examples/{tests,tutorials}/ to {tests,tutorials}/