Until recently, my e-library has consisted almost entirely of epub books from free sources. Last week a Kindle 3 came into my life

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I've had no problems converting and downloading my books to the Kindle. But I do have a question about synchronizing my Amazon book purchases, which are downloaded to my Kindle via Whispernet, bypassing my Calibre library, with my Calibre library.
Do I need to come up with a process to copy my Amazon purchases from my Kindle to Calibre? Is it a manual process, or can it be automated?