Nodal values can be brought into kernels, bcs.

Refs #4038
Migrating to coupledNodalValue interface

RichardsVarNames now uses coupledNodalValue.
RichardsPiecewiseLinearSink, RichardsBorehole, RichardsFullyUpwindFlux,
RichardsLumpedMassChange altered to use this.

Note that RichardsMaterial does not use this, but still calculates
things at quadpoints, even if only nodal quantities are required by BCs,
Kernels, etc.  I need to refactor this stuff and include a new
nodal-only Material, I think.

Closes #4038
Formatting according to code standards
Making MOOSE and modules compile when libmesh is configured --with-dof-id-bytes=8.

Refs #4321.
Add test harness option to restrict tests to specific
--with-dof-id-bytes configurations.

Restricting the aux_nonlinear_solution_from_xdr to only run when
libmesh has been configured with 4-byte dof ids.

Refs #4321.
Fixing 32/64bit conversion warnings found with -Wconversion

Refs #4321.
Allow overridding LIBMESH_DIR in update_and_rebuild_libmesh.sh
This commit allows the user to set LIBMESH_DIR in their environment and have it honored
when running update_and_rebuild_libmesh.sh. This will allow multiple installed
libmesh versions at the same time. Note that this script will not automatically
delete the contents of LIBMESH_DIR when set for the user's safety.

closes #4431
Merge pull request #4432 from permcody/override_libmesh_dir

Allow overridding LIBMESH_DIR in update_and_rebuild_libmesh.sh
Merge pull request #4400 from andrsd/nodal-values

Nodal values
Merge pull request #4429 from jwpeterson/64bit

Fixes for 64bit indices
Merge commit 'c77e7ae7215b62ae953807c08643ea9cfbcfd3c2'
Merge commit '55c3d700140e87fd8f8e44342a66dca73ccc80de'
Merge commit '20ea4e538ad47ada0e6ba2e0061ffb601218d3fb'