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Originally Posted by jxall
So there's no specific feature - either in KoboTouchExtended or Kepubify - to automatically fix this issue or batch-rename files?
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Not at the moment. KoboTouchExtended generates kepubs when sending books to the device. kepubify is really about doing the same thing. But the author has state he will add an option to generate the name as .kepub.
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And also, is there a specific reason why Kepubs are not natively supported by Calibre after all these years of development?
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Why would it? Kepubs are only used by Kobo ereaders. There is very little reason to keep a copy of them in the library. If you do get one from elsewhere with the extension as .kepub.epub, then it can safely be treated as an epub for just about everything.
And calibre is designed to be extensible using plugins. All the necessary plugins to support kepubs for those who want to store them exist. Just install them. The only issue is you need to drop the .epub from the name.