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Can I have jQuery and prototype loaded at the same time?

Yes, from version 0.6 onwards the plugin checks if both jQuery and Prototype are to be loaded and adds the relevant code to enable both to function together.

Why are some of my libraries are still loaded locally

The plugin will only switch libraries that have been loaded using the WordPress wpenqueuescript method. Any libraries that are hard-coded into theme headers or plugins will not be modified. If you are using a custom theme - consider loading your javascript using the wpenqueuescript method as this will also ensure that the library is not loaded more than once by other plugins, etc..

What libraries can be switched?

The plugin looks for and switches the following libraries: * Prototype * jQuery * Moo * Scriptaculous