Limiting tests to opt and oprof (closes #2653)
Deleting trailing whitespace missed by incomplete hook - #2460
Merge pull request #2660 from permcody/delete_whitespace

Deleting trailing whitespace missed by incomplete hook
Making sure solution vectors are in sync in AuxiliarySystem (closes #2659).

This patch moves the calls solution().close() and _sys.update() right
after the element and nodal loop.  It also adds the same calls inbetween
volumetric and boundary loops, which caused these two vectors to be out
of sync resulting in incorrect values used in auxiliary boundary
conditions.
Merge pull request #2658 from andrsd/sync-solution-vectors

Making sure solution vectors are in sync in AuxiliarySystem.
Repaired logic bug, added test for this bug, resolved ordering in OutputWarehouse (closes #2661)
Merge pull request #2663 from aeslaughter/recover-2661

Repaired [Outputs] related logic bugs
Merge pull request #2654 from aeslaughter/dbg-par-2653

Limits tests to opt and oprof
Removed PETSc types (closes #2665)
Merge pull request #2666 from aeslaughter/petsc-2665

Removed PETSc types
Move from gap to paired in name #2667
improve the getFE interface in Assembly #2668
enhance isNodal to allow more types of elemental variables #2668
Added guard for PETSc related calls
Dummy #000
Added inline ability for residual output (#2664)
Merge pull request #2672 from aeslaughter/iter-2664

Added inline ability for residual iteration output
better to move nodal variable check into the constructor #2668
Resolved creation of adapted mesh with oversampling (closes #2646)
Merge pull request #2673 from aeslaughter/orig-mesh-2646

Resolved creation of adapted mesh with oversampling, this is needed to get MARMOT completely updated.