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I would also recommend calibre as the goto version to manage / sideload any reading device you have. Even in the case of managing a DRMed library (if you only have one each of Kindle and epub reader) calibre is easy to use and works exactly the same on each computer (not just linux) and each different reading device. It is even possible to have a mixed library of DRMfree books, Kindle DRM, epub DRM in one place to search manage and organize all your books. Features like editing books or converting books to a different format will only work on DRMfree books, obviously.
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