First of all, congratulations for the great job. I love JabRef, particularly for its clean interface that at the same time incorporates many useful functions, but perhaps more important, because JabRef don't force users to store files in a particular place or way.
Now, one feature that I think would make JabRef even better is the ability to extract comments and highlighted text from a pdf file. Docear has implemented this function to work with a number of pdf-readers. In JabRef these annotations could be extracted in separated (or a single) fields, with (but preferable without, to keep it simple) the page where the annotation came from.
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