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 commit '959448c15b1b1b2a9f5b6c7f2e2e794dae57363a'
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
Merge commit '9836f6d326b32d65d2c50159b84902211d14ffb4'
Merge commit 'c9f649d11b9d6a82be388b661271ee30dc50fa3f'
Merge commit '404d4704cf6eed94bd4411b8e051de110a832032'