Tidy up javascipt

[davidmce]

Its getting pretty messy. Someone should clean it up...

[denics]

There is a lot to do with Javascript. Especially with the auto.js . For example, we can provide a static/javascript/auto with an empty 40_lightbox.js and 89_*.js to override the default one so that at least these two are not added to the auto.js file.

[davidmce]

I was reluctant to override much in an attempted to avoid breaking things. If it doesn't break stuff, the more overriding the better.