I run OpenSuse Tumbleweed in a VM. Running anything from a flatpak sandbox that needs to interact with other programs turned into a total PITA. I originally tried calibre from a flatpak and after a couple of days, I switched to using the install command line version. Sigil was not as bad in terms of broken functionality but I ended up building my own. Takes me back to the "good old days" of running Linux from floppies.
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