I'm fairly confident that it's a change in Flatpak itself rather than any one specific Flatpak, since all of my apps now use the same new screen sharing interface. Difference is that it actually works in those apps.
Were you using X11 before, by chance? IIRC Fedora 40 dropped X11, and only ships with Wayland by default. The fact that all of your apps are using the same screen sharing interface sounds like they’re using the screen share portal due to running under a Wayland session, which Discord doesn’t currently support currently.
For a while there was a workaround using a tool called XWaylandVideoBridge but even that stopped working for me.
I’ve heard that Vesktop supports screensharing under Wayland (and supposedly with sound support too), and it is available on Flathub - might be worth a try.
Use the Atomic variants from uBlue! This will make sure stuff like that happens on their servers, they fix it once and the users always get working updates. (Maybe with a day delay in cases like this)
In general avoid overwriting default files, as this .conf.d seems to be pretty standard. Your distro will handle the default .conf but may stop when you changed it manually.
What AI service did you use to get this? It doesn’t work, but ChatGPT (3.5) just told me to edit the xorg config to add tap-to-click (which I did but it didn’t do anything, probably because X11 is not installed)
KDE Discover supports Snap, Flatpak and distro packages (through PackageKit). It doesn’t support AppImage, though. It also doesn’t work very well outside of Plasma.
The metadata seems to be pretty close to full. I’m not using BTRFS, but I’ve read earlier that this is solved with rebalancing, or how is that called. Btrfs’s management command is able to do it.
But possibly the metadata is unreasonably large, so maybe the solution is not rebalancing.
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