The dark system theme I have set seems to make some applications look funny, with dark boxes where they should be light. Is there any way I can manually set a theme on a per-application basis?
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if you don't find another solution, i have libreoffice installed via flatpak and this issue does not exist
Because the theme doesn't get applied at all or why?
I don't know, stuff on the repos can be broken sometimes on some distros, i recall firefox on fedora with the missing codecs, opensuse and their flaky distrobox (or podman?) implementation.
In my experience, repo versions of software is not totally consistent, even worse when compared to flatpak, if a flatpak breaks, it doesnt break on just ubuntu, or fedora, or arch; it breaks everywhere, and gets fixed everywhere too. Credit where credit is due, small utilities generally tend to have better experience when installed natively, like htop, fish, and some other small programs.
Maybe i'm just a dumb software progressive, but flatpak generally is much more reliable for me than native repo versions of software.