math4 theme improvements

For the most part, these commits just continues the bootstrap integration: Bootstrap classes were added in appropriate locations and old interfering CSS was removed to let the default bootstrap styles appear. Minor restyling was done on items such as the top banner bar and the course listings.

There is one significant perl code change in the markup generated by the Main Menu. The Main Menu was changed from an h2 to a li element. Some level of nested ul was removed near the help/report bug part of the menu so that the main menu ends up being just one ul with nesting. I've tested that it doesn't break math3.

Most other perl code changes were things such as removing hard coded perl styles that was interfering with bootstrap.

Some quick screenshots: http://imgur.com/a/PhWSV