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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I had the same problem. It's been a while but I'm fairly certain the problem can be solved by installed the appropriate integration package. Try installing these packages,
libreoffice-plasmalibreoffice-qt5libreoffice-style-breeze. Take a look at this forum thread for more info, https://discuss.kde.org/t/libreoffice-does-not-honour-kde-theme/3347