Javascript cleanup

I've tried to make everything use one single version of jQuery (1.10.2) and jQueryUI (1.10.3). I think I've tested most major functionality, but there's probably some stuff I missed, so let me know if you see anything.

I've removed jQuery and jQueryUI from being loaded from the Sphinx directives in favor of including them once in the main layout files. This should theoretically mean that any future jQuery version upgrades will be much simpler.

I've also done some consolidation work on the various layout files that are being used with the new Bootstrap theme.