Remove broken link to bootstrap CSS

We include it directly from their CDN later in the file.
Load jQuery before bootstrap

The bootstrap JavaScript requires jQuery.
Remove IE 8 support

We wont be supporting that browser any time soon.
Remove double-included JavaScript
Remove more IE 8/9 compatibility code

From what I could find online, this code is there make IE 8 and 9 use
their best rendering engine to render the page. We don't support those
browsers anyway.
Close tags explicitly

This makes it easier for the nxml mode I use with Emacs to validate
the document.
Explict script type like the other elements