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FWIW, I have also raised this problem to the issue tracker https://github.com/flatpak/flatpak/issues/4151. The maintainer raised some good points too.
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the openRGB Flatpak, where you have to manually place a file into /etc/dev/rules.d/ because there is no way to access hidraw nodes from within flatpak. (the Steam Flatpak has similar issues)
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WorkOS
The modern identity platform for B2B SaaS. The APIs are flexible and easy-to-use, supporting authentication, user identity, and complex enterprise features like SSO and SCIM provisioning.
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the openRGB Flatpak, where you have to manually place a file into /etc/dev/rules.d/ because there is no way to access hidraw nodes from within flatpak. (the Steam Flatpak has similar issues)
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dino which needs access to the gpg-agent
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USB flashing applications like Balena Etcher and SpeedTest applications like KDiskMark which use PolKit to get higher privileges.
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For IDEs, what people do right now, especially on immutable distros like Fedora Silverblue, is use toolbx or Distrobox (it's like interacting and communicate with an IDE through a mutable distro, inside a container).
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InfluxDB
Power Real-Time Data Analytics at Scale. Get real-time insights from all types of time series data with InfluxDB. Ingest, query, and analyze billions of data points in real-time with unbounded cardinality.
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By default, Flatpak apps cannot read from xdg-config/gtk-3.0. Someone needs to provide that override out of the box on Plasma distros so that Flatpak GTK apps work as expected. FreeDesktop.org does not want to do it because they want a better mechanism to exist. And GNOME does not want to cooperate on making a better mechanism exist. GNOME being stalwart on their design vision does not make the problem go away. Other platforms have full color schemes. The two biggest GTK platforms forming an echo chamber to control the direction of FDO preferences doesn't change that.