Turn on checkbadSource test to generate an error when found; fix all source code that causes errors

Commit-type: portability-fix, testing-fix, style-fix, feature, maintainability
/spend 1.5h

DM: Nullspace constructor should report old and new field numbers

TS+Plex: Convergence estimation now working of time dependent PDEs
- Add exact solution time derivative to DS
- Put monitor in ConvEst for TS
- Fixed error determination in ConvEst for TS

Co-Authore

TS+Plex: Convergence estimation now working of time dependent PDEs
- Add exact solution time derivative to DS
- Put monitor in ConvEst for TS
- Fixed error determination in ConvEst for TS

Co-Authored-By: Brad Aagaard <baagaard@usgs.gov>

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Plex: Jacobian action now can use multiple DSes

Co-Authored-By: Brad Aagaard <baagaard@usgs.gov>

Plex: Move FEM assembly from dmplexsnes.c to plexfem.c, and fix DMCreateMassMatrix()
- Create regular mass matrix if we pass in the same DM to DMCreateMassMatrix()
- Changed DMPlexSNESGetGeometryFVM(

Plex: Move FEM assembly from dmplexsnes.c to plexfem.c, and fix DMCreateMassMatrix()
- Create regular mass matrix if we pass in the same DM to DMCreateMassMatrix()
- Changed DMPlexSNESGetGeometryFVM() to DMPlexGetGeometryFVM()
- Changed DMPlexSNESGetGradientDM() to DMPlexGetGradientDM()

Co-authored-by: Mark Adams <mfadams@lbl.gov>

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DM: Now DS stores exact solution functions for everything
- Added DMComputeExactSolution()
- DMSNES/TSCheck*() now use DS for functions

Merge branch 'stefanozampini/feature-add-hpackages-rebased' into 'master'

Fixes to MatProduct + many bug fixes + new hierarchical matrix support

See merge request petsc/petsc!2800

Plex: Labels stored in DM fields and DSes need to be refined during uniform refinement

Plex+SNES: Large update to support multiple DSes
- Now allow simple divisions of the domain with DMSetField()
- DMPlexComputeResidual_Internal() supports multiple DSes
- DMPlexComputeJacobian_Interna

Plex+SNES: Large update to support multiple DSes
- Now allow simple divisions of the domain with DMSetField()
- DMPlexComputeResidual_Internal() supports multiple DSes
- DMPlexComputeJacobian_Internal() supports multiple DSes
- DMSNESCheckDisretization() supports multiple DSes
- DMSNESCheckResidual() supports multiple DSes
- DMSNESCheckJacoiban() supports multiple DSes
- DMComputeL2FieldDiff() supports multiple DSes
- PetscConveEst supports multiple DSes
- Fixed bug refering to cStart from a cellIS
- Added PetscDSGetQuadrature()
- Added DMSetField_Internal()
- Added DMSetRegionNumDS()
- Protect PetscSectionView() from empty bcIndices
- ISDifference now allows a NULL second argument

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Fix misuse of PETSC_COMM_WORLD in library code

There are still many left, I'm tired of fixing them

[szampini@localhost petsc]$ git grep PETSC_COMM_WORLD | grep -v tests | grep -v tutorials | grep '

Fix misuse of PETSC_COMM_WORLD in library code

There are still many left, I'm tired of fixing them

[szampini@localhost petsc]$ git grep PETSC_COMM_WORLD | grep -v tests | grep -v tutorials | grep '\.c' | awk '{print $1}' | uniq
src/benchmarks/streams/CUDAVersion.cu:
src/benchmarks/streams/SSEVersion.c:
src/contrib/fun3d/comp/flow.c:
src/contrib/fun3d/incomp/flow.c:
src/dm/impls/forest/p4est/petsc_p4est_package.c:
src/dm/impls/moab/dmmbfem.cxx:
src/dm/impls/moab/dmmbmg.cxx:
src/dm/impls/moab/dmmbutil.cxx:
src/dm/impls/moab/dmmbvec.cxx:
src/dm/impls/moab/dmmoab.cxx:
src/dm/impls/network/network.c:
src/dm/impls/stag/stag.c:
src/dm/impls/stag/stag1d.c:
src/dm/impls/stag/stag2d.c:
src/dm/impls/stag/stag3d.c:
src/dm/impls/stag/stagda.c:
src/dm/impls/stag/stagutils.c:$
src/dm/impls/swarm/data_ex.c:
src/dm/impls/swarm/swarm.c:
src/dm/impls/swarm/swarm_migrate.c:
src/ksp/ksp/impls/fcg/pipefcg/pipefcg.c:
src/ksp/ksp/impls/gcr/pipegcr/pipegcr.c:
src/ksp/ksp/impls/gmres/pipefgmres/pipefgmres.c:
src/ksp/ksp/impls/tsirm/tsirm.c:
src/ksp/ksp/interface/itcreate.c:
src/ksp/ksp/interface/iterativ.c:
src/ksp/ksp/interface/saws/kspsaws.c:
src/ksp/pc/impls/bddc/bddcfetidp.c:
src/ksp/pc/impls/fieldsplit/fieldsplit.c:
src/ksp/pc/impls/gamg/util.c:
src/ksp/pc/impls/gasm/gasm.c:
src/ksp/pc/impls/is/nn/nn.c:
src/ksp/pc/impls/patch/pcpatch.c:
src/ksp/pc/impls/tfs/gs.c:
src/ksp/pc/impls/tfs/tfs.c:
src/ksp/pc/impls/tfs/xxt.c:
src/ksp/pc/impls/tfs/xyt.c:
src/ksp/pc/interface/precon.c:
src/mat/impls/aij/mpi/mpiaij.c:#define
src/mat/interface/matrix.c:
src/mat/interface/matrix.c:.
src/mat/interface/matrix.c:
src/mat/interface/matrix.c:$
src/mat/utils/multequal.c:
src/snes/interface/saws/snessaws.c:
src/snes/interface/snes.c:
src/sys/classes/draw/interface/drawreg.c:
src/sys/classes/random/interface/random.c:
src/sys/classes/random/interface/randomc.c:
src/sys/classes/viewer/impls/ams/ams.c:
src/sys/classes/viewer/impls/ams/amsopen.c:
src/sys/classes/viewer/impls/ascii/vcreatea.c:
src/sys/classes/viewer/impls/mathematica/mathematica.c:
src/sys/dll/reg.c:
src/sys/dll/reg.c:static
src/sys/dll/reg.c:
src/sys/error/adebug.c:
src/sys/error/checkptr.c:
src/sys/error/errstop.c:
src/sys/error/pstack.c:
src/sys/error/signal.c:
src/sys/ftn-custom/zutils.c:
src/sys/info/verboseinfo.c:
src/sys/logging/plog.c:
src/sys/logging/utils/eventlog.c:
src/sys/logging/xmllogevent.c:
src/sys/memory/mal.c:
src/sys/memory/mtr.c:
src/sys/objects/aoptions.c:
src/sys/objects/aoptions.c:+
src/sys/objects/aoptions.c:
src/sys/objects/ftn-custom/zstart.c:
src/sys/objects/ftn-custom/zstartf.c:
src/sys/objects/inherit.c:
src/sys/objects/init.c:
src/sys/objects/options.c:+
src/sys/objects/options.c:
src/sys/objects/pinit.c:MPI_Comm
src/sys/objects/pinit.c:
src/sys/utils/mpitr.c:
src/sys/utils/mpits.c:+
src/sys/utils/pbarrier.c:
src/sys/utils/pdisplay.c:
src/sys/yaml/yamlimpls.c:
src/sys/yaml/yamlimpls.c:+
src/sys/yaml/yamlimpls.c:
src/tao/pde_constrained/impls/lcl/lcl.c:
src/ts/interface/ts.c:
src/vec/is/is/utils/iscoloring.c:
src/vec/vec/impls/seq/seqviennacl/vecviennacl.cxx:
src/vec/vec/interface/vector.c:.
src/vec/vec/interface/vector.c:

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Plex: More hybrid fixes
- Converted hybrid assembly to use PetscTabulation
- Protect for NULL discretizations, which happen with no dofs for a field
- Added PetscDiscType enum
- Changed PetscDSIsFE_I

Plex: More hybrid fixes
- Converted hybrid assembly to use PetscTabulation
- Protect for NULL discretizations, which happen with no dofs for a field
- Added PetscDiscType enum
- Changed PetscDSIsFE_Internal() to PetscDSGetDiscType_Internal()
- Must inject coordinates from hybrid cells into the ambient space

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Plex+FE: Updates for hybrid integration
- Added support for hybrid Jacobians
- Added PetscDSHasBdJacobian()
- Added boundary Jacobian preconditioner
- Needed a path to integrate the hybrid Jacobian p

Plex+FE: Updates for hybrid integration
- Added support for hybrid Jacobians
- Added PetscDSHasBdJacobian()
- Added boundary Jacobian preconditioner
- Needed a path to integrate the hybrid Jacobian preconditioner
- Fixed indexing in hybrid element mat update
- Be careful about the difference between intrinsic dimension and embedding dimension for hybrid integration
- Need to use rectangular transformation of gradient in case they are different
- Fix use of embedding dimension
- Make sure FEGeom struct has the dimensions set
- Pointwise function derivatives are in the embedding space
- Use PetscArrayzero()
- Change TransitiveClosure() for hybrid cells
- We get the closures of the endcaps, and then the hybrid faces, this allows degenerate cells that we need in PyLith

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SNES: Replace 0 -> NULL for pointers

Plex: Prevent crash with no DS Jacobian functions set

Fix compile warning --with-log=0

Typos