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Installing it via "flatpak install foliate" didn't work? Downloading the .flatpakref seems like an unnecessary step to me but I'm on a different distro (openSUSE Tumbleweed).

edit: I can also open files from anywhere on my PC. Could it be that the flatpak on Debian Stretch is not correctly configured?

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I'm pretty sure your edit nails it: flatpak on my moldy Debian doesn't work correctly as a non-root user, and the alternative of running it as root and then running the application as a normal user was neither intended nor foreseen.

I did finally install Debian testing, and it looks like the flatpak problems are resolved, but I decided not to bother installing foliate because of the nearly 700MB of dependencies it wanted over my rural satellite connection. C'est la vie.

I went ahead and burned the data: for Science! After the dependencies were all downloaded, it works correctly and completely. It's a fairly nice ebook reader application, and it only took three days and replacing my operating system to get it.

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