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.
Console producing output with _allow_output = false (closes #3005)
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