The Choo framework is set up to replace the <body> with its render, but any <script> on the page when it's loaded should run—it just won't appear in the inspector after Choo renders.
EDIT: Unless you're talking about it surviving after saving the wiki, in which case it won't remain. I'm actively working on support for extending Feather Wiki that allows whatever custom JavaScript you want, in a very similar way to how the custom CSS is preserved. But it's not ready yet. Keep an eye out for version 1.3.0 in the near future!
EDIT: Unless you're talking about it surviving after saving the wiki, in which case it won't remain. I'm actively working on support for extending Feather Wiki that allows whatever custom JavaScript you want, in a very similar way to how the custom CSS is preserved. But it's not ready yet. Keep an eye out for version 1.3.0 in the near future!