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Why can't flatpaks just work
(lemmy.world)
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Some apps automatically pick up your theme some don't. For these I give the specific app access to my theme folder with a :ro at the end of the path.
IDEs should work ootb. If some extension doesn't work, maybe it's because of poor support for Flatpak. 9/10 times you'll find the issue is that app is calling the traditional /usr/bin path etc. when Flatpak installations use different paths.