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calibre settings are kept in the config directory ("$HOME/.config/calibre"). It doesn't matter where you install the program binaries, $CALIBRE_CONFIG will still be set to that by default. Although storing them in /opt is less messy than having them in your home directory, I'd think....
Why are you storing root-owned files in your home folder anyway?? The only reason I keep my calibre binaries in my home directory is because I am a non-root user on a school computer system.
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