DMForest: Turn off -dm_refine for now

Forest: Added DMCreateSubDM() support

DMForest: initialize more header functions when cloning

DMP4est: first pass at accounting for ghost cells

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/fe

Merge remote-tracking branch 'origin/knepley/feature-plex-add-time' into tisaac/dmforest

Both branches changeds DM projection behavior, so I wanted to sort it
out before merging

* origin/knepley/feature-plex-add-time: (59 commits)
SNES ex69: Updated to new function API, fixed test output
SNES ex75: Fixed for new function API
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fields
add -binary_write_double so __float128 precision can save as double to binary files
TSClone() did not clone Fortran function pointers hence some TS methods would fail if functions provided in Fortan
petsc4py: update to snapshot with 'barry/petscoptions-object' changes
fix bad merge that introduced 2 copies of the MPI_Comm_free()
update example to use MAT_INPLACE_MATRIX, not REUSE
incorrect addition of float to PetscInt
update for new PetscOptions API
TS ex18: Fixed function API and test output
Function now takes PetscOptions as first argument, this was missed during the first round of updates
bugfix for MatSetOption_Elemental()
fix test example no change output that was missing a line
fixes for new PetscOptions.. API that are needed based on problems with nightly build
Plex ex3: Use new function API
SNES ex62: Use new function API
SNES ex12: Use new function API
Plex: Fixed unused options in examples
Plex+DMDA: Add time to signatures
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DMForest: aliases for -dm_refine and -dm_refine_hierarchy to match DMPlex

DMP4est: ex12 almost runs clean.

- I had to fix some function namings in the DMP4est implementation.
- Every p4est connectivity needs a geometry in our implementation.
- Create DMShareDiscretization

DMP4est: ex12 almost runs clean.

- I had to fix some function namings in the DMP4est implementation.
- Every p4est connectivity needs a geometry in our implementation.
- Create DMShareDiscretization to indicate that a second DM is
essentially a different representation of the same data as the first,
and to allow them to have the same PetscDS related data.

There is still a problem with reference counting related to
{SNES,KSP,PC}->dm to work out.

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DMp4est: multilevel automatic hierarchy creation workin in snes ex12

DMP4est: some debugging towards automatic hierarchy creation

Once I was able to test hierarchy creation in ex12, I uncovered some
bugs in DMP4est related to constructing a connectivity from a plex,

DMP4est: some debugging towards automatic hierarchy creation

Once I was able to test hierarchy creation in ex12, I uncovered some
bugs in DMP4est related to constructing a connectivity from a plex,
naming of functions, etc.

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DMP4est: work on coarsening

1) We want the coarse mesh to inherit as many options as possible from
the parent, so there is now a DMForestTemplate() method for this type of
operation

2) Partitioning

DMP4est: work on coarsening

1) We want the coarse mesh to inherit as many options as possible from
the parent, so there is now a DMForestTemplate() method for this type of
operation

2) Partitioning for coarsening is a major p4est option, so I added it to
the DMP4est interface

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DM: add DMGet/SetFineDM

This requires the introduction of some cycle-detection when destroying a
DM.

DM: refine NonCyclicReferenceCounting

Only recurse in the event of a doubly-linked list. This

DM: add DMGet/SetFineDM

This requires the introduction of some cycle-detection when destroying a
DM.

DM: refine NonCyclicReferenceCounting

Only recurse in the event of a doubly-linked list. This is to let the
swapping that is used to create a DMPlex hierarchy keep working
unaffected.

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DMForest: introduce initial refinement level.

The idea being that, when a minimum and an initial refinement level are
specified, then a hierarchy is created that spans them, much like
-dm_plex_refin

DMForest: introduce initial refinement level.

The idea being that, when a minimum and an initial refinement level are
specified, then a hierarchy is created that spans them, much like
-dm_plex_refine_hierarchy.

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Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
remov

Merge branch 'master' into tisaac/dmforest

directory layout changed again: merging to switching branches back and forth
doesn't cause reconfigure to have a hard time

* master: (357 commits)
removed nonexistent ex46f from makefile test rule
Revert "fixed bad merge into master"
fixed bad merge into master
fix memory leak in mkl_pardiso fix some formatting in mkl_pardiso code
mv runex111 from TESTEXAMPLES_C to TESTEXAMPLES_DATAFILESPATH
Mat+Doc: More Fortran docs
Bib: Added TetGen cite
parmetis: make sure 'ldd libparmetis.so' points to the correct libmetis.so that its linked with.
small fix as reported by the nightly test
add a test for MatPtAP()
small cleanup; add tests
cleanup MatPtAPSymbolic_MPIAIJ_MPIAIJ()
Fix nonzerostate tracking in all MATMPI types.
update location of test matrices in faq.html file
unused variable still declared
Fix for MatLoad_MPIDense() from sparsely stored matrix also fix for MatLoad_MPIDense_DenseInFile() when matrix has not had its local sizes preset by user
Preserve the B nonzerostate during disassembly.
TSEvent: Fix arch-mswin nightly errors due to declaring variables in the middle of a function.
Fix error in parallel loading of dense format matrix
removed KSPSetNullSpace() since mat already carries that information and having two locations for it is confusing, unnecessary and prone to error added MatSetTransposeNullSpace() for providing the null space of the transpose of the matrix and added support in KSPSolve() to remove this null space from the right handside of the linear system thus making the system consistent.
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DMForest: make examples memory neutral

Update DMSetFromOptions_Forest() to include PetscOptions object

DMForest: able to generate and view some meshes with ex1

DMForest: start work on p4est/p8est implementation.

DMForest: proper include files so CMake can determine dependencies

DMForest: completion of most interface routines.

DMForest: some setup

Forest: try a minimal class