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"I don't know though if you can set it up to automatically work when the reader is plugged in..."
Not clear what you mean by "work". calibre manages your library. It can, for example, automatically copy any books in your Kindle directory into calibre, and convert them to other formats - for example, epub for a Sony.
When you plug in an e-reader, calibre will notice, and will show which books are loaded in the reader. If you have new books, you select them and tell calibre to load them into the reader.
"They say it's automatic, but really, you have to push this button..."
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