I'm a developer of an open source program but have no idea how to properly distribute binaries to Linux users

https://zquestclassic.com/

Discussions: https://discu.eu/q/https://zquestclassic.com/

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Answer: you don't

#Flatpak would be great and generally works across distros.

It's missing the trust issue though. Better just to make the source and buildfiles available then the distros can package it as necessary themselves.

The alternative to Flatpak is Snap. Both act similar to distributing a running executable.

appimages too, they are better because they are standalone