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Vanilla and Scriptaculous (Read it Mark :P)
Ok, so I'm working on an extension which uses the prototype/effects library. But when checking the javascript files I came to notice they are kind of old! I could add the files to my extension, but shouldn't it be updated in the core?
How to deal with this?
How to deal with this?

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with jquery 1.1.3 just about to come out, Resig said that he is overhauling the animation and effect library of jquery plus speed improvement to its selectors.
You can file them with you extension or give instructions for updating.
There are so many more things to think about other than file size when dealing with serving speed:
http://www.thinkvitamin.com/features/webapps/serving-javascript-fast
I'm an advocate of Mootools, despite it's prima donna developer, but it'd require a lot of rewriting of the AJAX sort of parts of Vanilla.