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.
Merge pull request #3076 from jwpeterson/doc_fixes

Doc fixes