fixup doxygen css  #2460
Checking for return codes in build libmesh script - #2460
Merge pull request #2611 from permcody/script_update

Checking for return codes in build libmesh script - #2460
Fix TestHarness error

The --pbs option, when reporting status, couldn't handle a negative status
code.  This fixes that.  #2612
Merge pull request #2614 from jasondhales/testharness_2612

Fix TestHarness error
Moving modules tests - #2460
Merge pull request #2619 from permcody/move_tests

Moving modules tests - #2460
Moving a few more tests - #2460
Merge pull request #2621 from permcody/move_tests2

Moving more tests - also testing whitespace hook, and ticket hook
Fixing bug in water_steam_eos module - #2460
Merge pull request #2622 from permcody/water_steam_eos_fix

Fixing bug in water_steam_eos module - #2460
Fixup syntax page generation refs #2460
Merge pull request #2623 from friedmud/syntax_2460

Fixup syntax page generation refs #2460
Add GNUPlot outputter (#1927)
Added SolutionHistory outputter (#1927)
Updated Input Files (#1927)
Various framework changes in suport of input file updates (#1927)
Moved OutputWarehouse object to MooseApp (#2563)

Conflicts:
	framework/include/outputs/OutputBase.h
Recovery now fully-functional with Outputs (#1927)
Fixing typos and coding style (Merged from andrsd; #1927)