Correction needed for YAK (refs #4389)
Merge pull request #4392 from aeslaughter/bug-4389

Correction needed for YAK
Implemented 'output_on' for output system (refs #3847)
Added ability to disable and force output so MultiApp output operates correctly
(refs #3847)
Updated gold for test that had repeated final output (refs #3847)

-------------------------------------------------------------------------------
OLD GOLD HAD REPEATED TIME STEP: ncdump gold/master_out_sub0.e
-------------------------------------------------------------------------------
 time_whole = 0, 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.1,
    0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.2, 0.21, 0.22,
    0.23, 0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.3, 0.31, 0.32, 0.33, 0.34,
    0.35, 0.36, 0.37, 0.38, 0.39, 0.4, 0.41, 0.42, 0.43, 0.44, 0.45, 0.46,
    0.47, 0.48, 0.49, 0.5, 0.51, 0.52, 0.53, 0.54, 0.55, 0.56, 0.57, 0.58,
    0.59, 0.6, 0.61, 0.62, 0.63, 0.64, 0.65, 0.66, 0.67, 0.68, 0.69, 0.7,
    0.71, 0.72, 0.73, 0.74, 0.75, 0.76, 0.77, 0.78, 0.79, 0.8, 0.81,
    0.820000000000001, 0.830000000000001, 0.840000000000001,
    0.850000000000001, 0.860000000000001, 0.870000000000001,
    0.880000000000001, 0.890000000000001, 0.900000000000001,
    0.910000000000001, 0.920000000000001, 0.930000000000001,
    0.940000000000001, 0.950000000000001, 0.960000000000001,
    0.970000000000001, 0.980000000000001, 0.990000000000001, 1, 1 ;

-------------------------------------------------------------------------------
EXODIFF OF OLD GOLD AND NEW FILE, EXCLUDING THE FINAL DUPLICATED TIMESTEP
exodiff -steps="1-101" gold/master_out_sub0.e master_out_sub0.e
-------------------------------------------------------------------------------
   *****************************************************************
              EXODIFF	(Version: 2.69) Modified: 2013-07-11
              Authors:  Richard Drake, rrdrake@sandia.gov
                        Greg Sjaardema, gdsjaar@sandia.gov
              Run on    2014/11/13   10:59:30 MST
   *****************************************************************

Reading first file ...
Reading second file ...
  FILE 1: /Users/slauae/projects/moose/test/tests/transfers/transfer_interpolation/gold/master_out_sub0.e
   Title: master_out_sub0.e
          Dim = 2, Blocks = 1, Nodes = 121, Elements = 100, Nodesets = 4, Sidesets = 4
          Vars: Global = 0, Nodal = 4, Element = 1, Nodeset = 0, Sideset = 0, Times = 102

  FILE 2: /Users/slauae/projects/moose/test/tests/transfers/transfer_interpolation/master_out_sub0.e
   Title: master_out_sub0.e
          Dim = 2, Blocks = 1, Nodes = 121, Elements = 100, Nodesets = 4, Sidesets = 4
          Vars: Global = 0, Nodal = 4, Element = 1, Nodeset = 0, Sideset = 0, Times = 101

exodiff: WARNING First file has 102 result times while the second file has 101.

exodiff: WARNING First file has 102 result times while the second file has 101.

Coordinates will be compared .. tol:    1e-06 (absolute), floor:        0
Coordinates will be compared .. tol:    1e-06 (absolute), floor:        0
Time step values will be compared .. tol:    1e-06 (relative), floor:        0
No Global variables on either file.
Nodal variables to be compared:
      u                                tol:    1e-06 (relative), floor:        0
      nearest_node                             1e-06 (relative),               0
      mesh_function                            1e-06 (relative),               0
      interpolation                            1e-06 (relative),               0
Element variables to be compared:
	user_object                      tol:    1e-06 (relative), floor:        0
No Element Attribute variables on either file.
No Nodeset variables on either file.
No Sideset variables on either file.

  ==============================================================
  NOTE: All node and element ids are reported as global ids.

  --------- Time step 1, 0.0000000e+00 ~ 0.0000000e+00, rel diff:  0.00000e+00 ---------
Nodal variables:
Element variables:

exodiff: Files are the same
         The number of timesteps are different but the timesteps that were compared are the same.
Updated DOFMapOutput to operate using 'output_on'
(refs #3847)
Created tests for DOFMapOutput
(refs #3847)
Disable deprecated messages during applyParameters calls, which avoids crazy message printing from common parameters
(refs #3847)
Disabled phase-field test
(refs #3847)
Updated input files for new 'output_on' syntax
(refs #3847)
Update modules input files for 'output_on' syntax
(refs #3847)
Restrict a check_error (warning) test that is getting mixed up
(refs #3847)