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Try using Stylepak, then.
Flatpak essentially decouples OS level packages from (GUI) App packages, and this is radically different to "unix way" and some people freak out of it. Flatpak is primarily meant for "apps" (those having GUI and used by users), not for "services", "libraries" and alike things. I love flatpak because: - I (as a user) have no time to keep eye on every app on my system, update and build it from source each time it updates/releases (I have family and work to do, no time for this). - developers (of apps) have no time to adapt their dependency libraries to match every linux distro out there (this usually causes that some GUI app cannot be built, or is very painful to build on some given distro). - distro developers have no time to adapt every included app library dependencies to match their own distro library versions (this usually causes that distros "freeze" their own shipped GUI apps to some, usually "ancient" version). - disk is cheap. So, flatpak is for rescue: - is ideal for GUI Apps, is not meant to replace system packager (like rpm, apt, etc). Think "libreoffice" and alike apps. - it uses libostree (one can say "git for binaries") https://ostreedev.github.io/ostree/ - apps are (ideally) packaged alone (no libraries included, unlike AppImage for example) but with declared dependencies, and dependencies are downloaded automatically by flatpak - this means there is no duplication (in case app A and B both use some "lib", that lib is downloaded only once and is shared) - this also means there IS "duplication" in case installed app requires different plaf or library versions (in case app A wants lib 1.0 and app B wants lib 1.1, both lib 1.0 and lib 1.1 will be downloaded). Once dependency is gone (as app A updates to lib 1.1), the lib 1.0 is purged as well (removed from your disk). Personally (while on Linux Mint) I tried to: - install base OS and Cinnamon DE from distro provided packages and reposes (deb packages) - keep OS package tree as clean as possible (so no custom reposes, no PPAs etc) - install all GUI Apps from flatpaks (and Linux Mint udpdate manager kept them up to date) Sadly, Linux Mint flatpak support was lagging way too much from mainstream. Since on Fedora 36, this almost happens automagically.
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