Added DMCoarsenHook_Coordinates() to push user coordinates down MG/FAS hierarchy

Nonlinear problems with a user-set coordinate vector now work with rediscretization multgrid.

Very incomplete work on adding DMLocalToLocalBegin()/End() operations.

DM: It looks like over-aggressive compilers did not perform this initialization if the loop never executed

logging memory now credits to all ancestors

DM: During DMDestroy(), clear out known compositions to avoid circular ref
- These come from FS

Fix VecSetDM() to accept dm=NULL

DMMesh: Removed all trace and salted the earth, Carthago delenda est!

Merge branch 'barry/fix-xxxviewsetfromoptions'

* barry/fix-xxxviewsetfromoptions:
*ViewFromOptions: update documentation, providing disabled man pages
fixed bug where XXXViewFromOptions() used p

Merge branch 'barry/fix-xxxviewsetfromoptions'

* barry/fix-xxxviewsetfromoptions:
*ViewFromOptions: update documentation, providing disabled man pages
fixed bug where XXXViewFromOptions() used prefix of object rather than appropriate prefix of KSP or SNES

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Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: Fixed bug in DMPlexOrient() - Must visit faces in BFS order so that all comparisons are in a connected component of the mesh
DM: Fix leak

Merge branch 'knepley/pylith'

* knepley/pylith:
DMPlex: Fixed bug in DMPlexOrient() - Must visit faces in BFS order so that all comparisons are in a connected component of the mesh
DM: Fix leak when creating global section
DMPlex: Fix allocation for embedded submesh
DMPlex: Removed debugging prints
DMPlex: Fix leak in interpolation
DMPlex: Added DMPlexOrient() which correctly orients a set of adjacent cells - You need this when extracting an embedded submesh
DMPlex: Fix memory management in submesh creation

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DM: Fix leak when creating global section

*ViewFromOptions: update documentation, providing disabled man pages

Most uses for these functions are to place diagnostics in the main
execution flow rather than placing it in a normal *SetFromOpti

*ViewFromOptions: update documentation, providing disabled man pages

Most uses for these functions are to place diagnostics in the main
execution flow rather than placing it in a normal *SetFromOptions
function that is only executed once. This commit provides documentation
because the old comments were incorrect, but does not generate man pages
because we'd rather not encourage users to choose this interface.

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fixed bug where XXXViewFromOptions() used prefix of object rather than appropriate prefix of KSP or SNES

Doc fixes for DM Hooks

Merge branch 'prbrune/dmda-subdomains-per-process'

Conflicts:
src/dm/impls/da/dadd.c

SF: define MPIU_REPLACE to work around missing MPI_REPLACE

removed unnneeded and unused XXXRegisterDestroy() routines

removed PetscFunctionListDestroyAll() and put PetscFunctionListDestroy(&XXXList) into the package finalize

PetscSF: split petscsftypes.h out of petscsf.h

Callers of PetscSF functions must now explicitly include petscsf.h.

Merge branch 'jed/functionlist-nocast'

* jed/functionlist-nocast:
docs: simplify explanation of function lists/composition
PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast
P

Merge branch 'jed/functionlist-nocast'

* jed/functionlist-nocast:
docs: simplify explanation of function lists/composition
PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast
PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast
PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

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Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add t

Merge branch 'barry/rm-xxxregisterdynamic'

* barry/rm-xxxregisterdynamic:
Registration: remove stale 'XXRegisterDynamic)' entries in man pages
TS examples: fix use of PetscFunctionList and add to nightlies
Changes: Note updates to XRegisterDynamic/PetscObjectComposeFunctionDynamic
PetscObjectComposeFunctionDynamic: remove stale docs and usage
developers.tex: remove complications from function composition with dlls
removed string version of function name for XXXRegister(), PetscFunctionListAdd() and PetscObjectComposeFunction()
changes: document PetscFunctionListAdd() API change
developers.tex: update documentation of PetscObjectComposeFunction
removed path and MPI_Comm arguments from PetscFunctionListFind/Add()
removed path argument to XXXInitializePackage() and XXXRegister()
removed XXXRegisterDynamic() but kept the APIs for everything else underneath the same phase I of the update to handling registering function pointers

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Merge branch 'tautges/dmmoab'

* 'tautges/dmmoab'
DMMoab: Remove OBJSC from makefile
TS ex30.cxx: write output file matching example number (ex30-final.h5m)
DMMoab: alltest run TS ex30
DMMoab

Merge branch 'tautges/dmmoab'

* 'tautges/dmmoab'
DMMoab: Remove OBJSC from makefile
TS ex30.cxx: write output file matching example number (ex30-final.h5m)
DMMoab: alltest run TS ex30
DMMoab: ops pointers initialized in DMCreate_Moab
DMMoab: fix test example makefile
DMMoab: close memory leaks by explicitly calling C++ destructors
DMMoab: interface does not require that all of PETSc be built using C++
DMMoab: include <sstream> to use ostringstream
DMMoab: do not mix CHKERRXX() with CHKERRQ()
Fixing uninitialized memory, and adding output.
Fixing compile error in dmmoab.
Changes suggested by Jed and Barry.
Changes suggested by Matt in pull request.
Adding DMMoab and VecMoab, along with various examples and tests.

Conflicts:
src/ts/examples/tutorials/makefile

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PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast

Rationale is the same as the parent. This makes all of
PetscFunctionListAdd(), PetscFunctionListFind(),
PetscObjectComposeFunction

PetscObjectQueryFunction: use macro to hide PetscVoidFunction* cast

Rationale is the same as the parent. This makes all of
PetscFunctionListAdd(), PetscFunctionListFind(),
PetscObjectComposeFunction(), and PetscObjectQueryFunction() consistent
regarding function pointer return types.

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PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast

Same rationale as the last commit:

Casting using PetscVoidFunction instead of (void(*)(void)) is needed
with C++ compilers that will

PetscFunctionListAdd: use macro to hide (PetscVoidFunction) cast

Same rationale as the last commit:

Casting using PetscVoidFunction instead of (void(*)(void)) is needed
with C++ compilers that will not implicitly convert C++ language linkage
to C language linkage. Since PetscFunctionListAdd() is meant to operate
on generic function pointers, we hide this language linkage detail
(which is inconsistently implemented) in a cast.

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PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

Casting using PetscVoidFunction* instead of (void(**)(void)) is needed
with C++ compilers that will not implicitly convert C++ lang

PetscFunctionListFind: use macro to hide (PetscVoidFunction*) cast

Casting using PetscVoidFunction* instead of (void(**)(void)) is needed
with C++ compilers that will not implicitly convert C++ language linkage
to C language linkage. Since PetscFunctionListFind() is meant to operate
on generic function pointers, we hide this language linkage detail
(which is inconsistently implemented) in a cast.

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Fortran: callbacks cannot use auto-generated interfaces