Update to Bootstrap 3.3.1

This PR updates from Bootstrap 2.3.2 to Bootstrap 3.3.1.

Some notes:

* Bootstrap 3 requires some shims to work with IE8. Ideally these shims are loaded in conditional comments as shown [here](http://getbootstrap.com/getting-started/#template), but I don't think pandoc's `self-contained` output supports inlining resources that are in conditional comments. So instead the shim files are always loaded, but the code is only actually run in IE8 (see the commit with comment `Make shims run only in IE`).
* Many of the themes changed fonts, and all of them switched to the .woff file format.
* The default.html template didn't seem to need any updates to work with Bootstrap 3. (http://getbootstrap.com/migration/)
* The file `bootstrap-responsive.min.css` is no longer in Bootstrap; version 3 has responsive code built-in.
I guess after we take this PR interactive documents will require the newer version of Shiny. As a result perhaps we should time the merge with after Shiny master merges bootstrap 3 (or perhaps it already has?)