A working version of PBS functionality. Still need to tally launches correctly. References #4114
Using jacobian caching in computeFullJacobianThread

Removing ComputeFullJacobianThread::postElement, thus using its parent's
implementation that has jacobian caching. Also, added caching of
contributions coming from scalar variables.
Moving the if-statement in DGKernel outside computeOffDiagJacobian

It was inside the most inner loop, but it should be outside
(performance!).
Fixing a typo
Do not check the emptiness of DGKernelWarehouse 3 times.

Once is just enough ;-)
Added missing call to prepareFaceShapes

This was causing an issue in a threaded run, where the shape function
values were not computed and the jacobian contribution ended up being
zero.

Closes #4109
Removing abandoned input file

This file seems to be in tests/userobjects/side_user_object_boundary_id
Running the test only with 1 thread

The test seems to be stable, but with 4 threads, it sometimes gives a
slightly different answer (~ 1e-2 rel. tolerance). This might be caused
just by different order of floating point operations, because the test
would sometime pass even with 4 threads.  However, marking it just for
serial runs.
Don't use CLI overrides in subapps
closes #4117
Merge pull request #4115 from milljm/pbs_fix

A working version of PBS functionality
Merge pull request #4116 from andrsd/jacobian-threading-issue

Fixing various issues
Default Transfer execute_on to match associated Multiapp
closes #4001
Merge pull request #4118 from permcody/cli_sub_app_override

Don't use CLI overrides in subapps
Remove python 2.7 syntax from get_repo_version.py
refs #4026
Merge pull request #4120 from permcody/transfer_exec

Default Transfer execute_on to match associated Multiapp