Ignore warnings from VTK header files.

Refs #1777.
Fixing a few signed/unsigned comparison warnings.

Refs #1777.
Modified FiniteStrainCrystalPlasticity #3607

Added and regold tests #3607
Merge pull request #3687 from jwpeterson/fix_warnings

Fix warnings
Fill in _objects_by_name for constraints to enable multi-threaded runs (closes #3690)

When a constraint is added, we have to add the MOOSE object pointer into
the _objects_by_name array for thread 0 (which we correctly do). But we
also have to add an empty array for the given name for threads with TID
> 0. That way the call to getObjectsByName() is not broken for calls
with TID > 0.  It mistakenly reports 'no object of a given name', but
the object is there, just not for the given thread.
Merge pull request #3665 from cpritam/feature_3607

Feature 3607
Merge pull request #3691 from andrsd/mt-constraints

Fill in _objects_by_name for constraints to enable multi-threaded runs (...
Declare 'unsigned int' consistently with rest of MOOSE.

Refs #1777.
Make J Integral tests more tolerant of machine differences ref #3633

For these tests, the nonlinear residual won't drop any lower than
about 5e-4, which translates to a relative tolerance of about 1e-8.
The domain integrals are pretty sensitive to small differences in
the solution, so I've had to use pretty loose tolerances to get
this test to pass cross-platform, and it's still been problematic.

I've tried a lot of things to try to get this to converge tighter,
and haven't found anything that makes a difference.

That convergence floor seems to be independent of the load, so I
increased the loading by a factor of 1000, which permits solving
to a much tighter relative tolerance.  I also made these use the
default setting for pc_hypre_boomeramg_strong_threshold.
Check for "unidentifed nominuses" in input files

Refs #3683.
Fixing buggy input files found while working on #3683.

There is a new (improved) error message to check for when parsing
checked_pointer_param_test.i
Merge pull request #3694 from bwspenc/fix_jint_tests

Make J Integral tests more tolerant of machine differences
Add option to action to output variable values along crack ref #3671

This adds the parameter 'output_variable', which the user can specify
to create PostProcessors that output the values of variables along
the crack.  The naming scheme of those PostProcessors matches that of
those used to calculate domain integrals.  This will allow comparing
toughness to stress intensity at locations along the crack.
Display initial adaptivity progress
(closes #3703)
Merge pull request #3704 from aeslaughter/progress-3703

Display initial adaptivity progress
Merge pull request #3700 from bwspenc/crack_var_action

Add option to action to output variable values along crack
Merge pull request #3697 from jwpeterson/parser_nominus

Add extra input file checking to Parser
Change error message as suggested by @bwspenc

Refs #3683.