Check return code when calling subprocess and throw better error
closes #2898
Test reading a Gmsh file with BCs

The test reads a Gmsh file with lower-dimensional elements
which specify BCs, and solves a Laplace problem on that mesh.

Refs #1402.
Restricing test
refs #2972
More operator spacing for #2951
Calculate gradient normal direction wrt PBCs.
Fixing my bad typing - refs #2972
make eigen executioners more modular #2983
fix gold files due to timing changes #2983
remove the exec_custom business #2983
Size stateful neighbor materials - refs #2972
Change the behavior of --mesh-only slightly.

When a filename is not provided, or when an Exodus file is requested,
we now write it using the "logical" dimension of the Mesh rather than
the spatial dimension (which is the default).  This helps us better
support visualizing 2D triangular meshes in peacock, since they will
now show the correct sidesets.

Interestingly, this did not require regolding any of the --mesh-only
MOOSE tests, since they were all already 3D.  But you can see the
issue if you open $MOOSE_DIR/test/tests/mesh/gmsh_bcs/plate_hole.msh
in peacock before and after the patch.

Refs #1568.
Update peacock for default name change (#2609)
Addresses issue #2927 .  Ability to bound variables during nonlinear solve.  Note, this only works for two phase problems at the moment - multiphase is not a difficult generalisation, but i have not yet worked out what actually needs to be bounded, and also i have not yet thought about the user interface for the multiple kinds of bounding that are possible.  **THERE ARE POTENTIAL BUGS IN RichardsMultiphaseProblem.C REGARDING THREADS AND/OR PARALLELISM THAT I WOULD LIKE SOMEONE TO CHECK**  Note that compared with the previous PR i have used local_nodes_begin and local_nodes_end - this gets around segfaults in multiproc jobs but i don't know if it is correct.  Derek has OKed this stuff, and has suggested changes: checking order, family and isnodal; using _mesh; some comments re .close.
Dummy commit - testing new moosebuild steps #000
Using MOOSE_COLOR to control coloring during test_subs
closes #3001
EigenKernel should not change eigenvalue is it presents #3007
Addresses issue #3009 .  gh_bounded_17 test previously failed in dbg mode due to a division by zero since there was zero gas present, so a mass balance for gas did not make sense
Testing multi-step PR and devel_to_master scripts
refs #000
Guard VTK, Exodus, and Nemesis Outputs.

Refs #3015.
Get the _real_ path pf cluster_launcher. References #3017