Javascript ignored after page transitions - what do you do?

Javascript ignored after page transitions - what do you do?

How is everyone working around the fact that when using Ajax transition (swipes), you cannot execute any JS on the following page?

On my first app I simply resorted to using rel="external", but for my second app I'd really prefer to take advantage of the swiping to give a native feel. The external links work fine, but that brief flash of white while the next page loads is not very appealing.

However, I simply cannot get around this problem and searching does not turn up any solutions, only more headaches. Any recommendations? This seems like a fundamental flaw, and unless everyone is developing applications that are static or doesn't require JS on each page, what are people doing?