Re-order application of elemental and scalar to nodal variables (#2663)

Added ability to disable intermediate time steps (#2633)

Added tests for intermediate output (#2663)
Merge pull request #2697 from aeslaughter/update-2633

Minor tweaks to [Outputs] needed for updating INL herd
Merge commit '3d179d949139b0f2ca6975b02131e0aa07188ff3'