Removing unused Makefile.elkunit

Remove mentions of Elk from some Makefiles.

Refs #2936.
Fixes to LaTeX syntax in Doxygen docs.

Refs #2986.
Ignore html files from Doxygen in git.

Refs #2986.
Running doxygen -u on modules Doxyfiles.

Refs #2986.
Point to framework and modules correctly in Doxyfiles.

Refs #2986.
dont use sparsity pattern and fix some jacobian entries for mechanical contact refs #2143 #2816
Console producing output with _allow_output = false (closes #3005)
Merge pull request #3073 from friedmud/contact

dont use sparsity pattern and fix some jacobian entries
Merge pull request #3075 from jwpeterson/remove_elk

Removing unused Makefile.elkunit
Merge pull request #3076 from jwpeterson/doc_fixes

Doc fixes
Merge pull request #3077 from aeslaughter/allow-3005

Console producing output with _allow_output = false
Fixes #3078 .  I have extended SideSetsAroundSubdomain to include optional specification of a normal direction.  This involved a lot more screwing around than i anticipated.  Amend: got rid of a tab.  Amend: corrected supid programming involving Point.  Amend: normal -> _normal in constructor.
Fixing Makefile bug where it couldn't find build.mk if MOOSE_DIR wasn't set
refs #3058
Disabling test in recover (#3082)
Fixing memory leak introduced by b552200 (closes #3050)
Merge pull request #3084 from andrsd/fix-memory-leak

Fixing memory leak introduced by b552200 (closes #3050)
Merge pull request #3081 from permcody/makefile_fix

Fixing Makefile bug where it couldn't find build.mk if MOOSE_DIR wasn't ...
AuxKernel creation uses restrictable interfaces (closes #3014)
Merge pull request #3079 from WilkAndy/feature_3078

Fixes #3078 .  I have extended SideSetsAroundSubdomain to include option...
Merge pull request #3085 from aeslaughter/auxkernel-3014

AuxKernel creation uses restrictable interfaces