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Originally Posted by JSWolf
1. Really bad idea. Someday you could end up having to start from scratch.
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To be more specific, JSWolf is referring to the possibility that an update could change how the users table is handled in a way incompatible with the hack, causing a sign-out at best and an automatic full reset at worst.
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4. Ditching Calibre will lose you so much automation and you'll lose the editor, viewer, easy eBook management, and a lot of other really useful features (including being able to remove DRM).
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To be fair, I automate everything without Calibre (and prefer to edit my ebooks from the command line). DRM removal doesn't require Calibre (and IIRC, the tools won't even work with py3 in the latest version of Calibre). It's really up to preference.
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As for kepubify, there's an issue with hyphenation with KePub. That has been fixed in the KoboTouchExtended driver for Calibre.
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And in kepubify v3.1.6.