Mat: remove third argument to MatNullSpaceRemove

Out of place removals were dangerous because the MatNullSpace held the
only reference to the resulting Vec, which is dangerous.  This use case
is rare (never used in PETSc itself) and can easily be accomplished:

  VecDuplicate(x,&y);
  VecCopy(x,y);
  MatNullSpaceRemove(nullsp,y);

Suggested-by: Tobin Isaac <tisaac@ices.utexas.edu>
Mat: remove 'vec' member of MatNullSpace

We no longer support out-of-place removal, so this field is only
relevant in MatNullSpaceTest.  Might as well simplify the data structure
and free the memory earlier.
SNES: call SNESLineSearchGetSuccess before using result in PetscInfo

Microsoft's compiler warns about this use of an uninitialized variable.
SNES VISS: remove stale linesearch comment
moved GAMG log registers to pachage init.
PCGAMG: set bjacobi->same_local_solves=TRUE to clean coarse grid viewing

When bjacobi->same_local_solves=FALSE, PCView_BJacobi views each
subdomain solver separately.  (That output is currently jumbled because
singleton viewers does not produce synchronized output, but O(P) data in
a -ksp_view is still not acceptable.)  GAMG configures all local solves
identically (though all but one process will have zero entries) but in
doing so, it trips bjacobi->same_local_solves=FALSE.  This commit is a
temporary fix until PCView_BJacobi is fixed to recognize this situation
in a more general setting.
PCBJacobi: call KSPSetFromOptions(subksp) when PCSetUp was called first

Prior to this patch, -mg_coarse_sub_pc_ options were never parsed when
using PCGAMG, which changes the coarse solver and calls
PCSetUp_BJacobi_Singleblock so that PCBJacobiGetSubKSP is available.
SNESFAS: protect SNESView on smoothers before creation in SNESSetUp

When SNESView_FAS is reached before SNESSetUp or SNESSolve, the
smoothers have not been created yet, resulting in attempted
SNESView(smoothd=NULL,viewer).  Instead, just say they aren't available
yet.

Noticed-by: Patrick Farrell <patrick.farrell@imperial.ac.uk>
SNESView: notify user when SNES has not been set up yet

Suggested-by: Peter Brune <brune@mcs.anl.gov>
TS: add TSRHSJacobianSetReuse, fixes TSComputeRHSJacobianConstant

When using a constant RHS and no IJacobian, the RHS Jacobian is shifted
to make it function as an IJacobian (shift*I - Arhs), which is the matrix
used by SNES.  We don't want to duplicate the full matrix because that
uses a lot of memory, so we play this game of recording the shift and
scale, then unshifting in TSComputeRHSJacobian.  Add tests that fail
prior to this bug fix.
TS tests/ex5*: re-activate test and fix monitor interval

The test was broken in 605b8b3063496ded55fa9a when support for periodic
monitoring was removed.
TS tests/ex3: fix example and inclusion in nightlies
TS: fix shortcut scaling; document TSComputeIJacobianConstant limitations

The shortcut re-shifting on re-evaluation of the IJacobian can only be
used when the implicit system is just the "mass matrix".  This
re-scaling also needs to be recorded for the next iteration.  Since this
logic cannot work in general, it is now moved to
TSComputeIJacobianConstant.  This funtion seems to be of limited use
beyond "explicit" finite element computations (especially those that use
a consistent mass matrix) and similar.
TS tests/ex3: SNESFD and TSComputeIJacobianConstant are incompatible
KSP: add man pages for pipelined CG/CR methods
KSP: add FAQ on efficient execution of piplined methods

Reference from the man pages of the pipelined KSPs, though unfortunately
I don't know how to mark-up a hyperlink.
TS: fix MSVC compiler error: non-POD member of anonymous struct

Suggested-by: Jed Brown <jedbrown@mcs.anl.gov>
download MOAB with git if possible
fix missing ierr when setting moab citations
Merge branch 'barry/xolotl'
Merge branch 'barry/citations' into barry/xolotl

Fix double-addition of 'ierr'.

* barry/citations:
  dmmoab: fix compile error