I think it'd probably be best to convert on an 'as needed' basis. Converting a single book can take up to 30 seconds depending on the size of the book. Doing so on an entire directory could take a lot of time.
I belive that once you open the book, it's automatically added to FBReader's library. But to be honest, the script would work best if called from the contentlister. And if you're using the contentlister to open books in FBReader, the library function isn't really necessary. Once iRex updates the contentlister for easy 3rd party reader support, things will be much easier.
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