Flatpak permission issues

Lately, I've been having some issues with running most of my Flatpak apps.
It seems to be related to Vulkan and the inability to create files in /usr (which it shouldn't).

I've tried repairing flatpak, tried reinstalling apps with system or user with no luck. I tried rolling back to F40 with no luck then rebased to stable again. Everything should be up to date (using

ujust upgrade

ujust upgrade

). I've tried researching with no luck, I might have to wipe and install bazzite again but I hope I don't have to go that route.

Here's an example where protontricks fails to run:

 Nov 19 19:01:57 bazzite systemd[2603]: Started app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service - Protontricks.
Nov 19 19:01:57 bazzite flatpak[36337]: bwrap: Can't mkdir /usr/lib/extensions/vulkan: Read-only file system
Nov 19 19:01:57 bazzite flatpak[36332]: error: ldconfig failed, exit status 256
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Main process exited, code=exited, status=1/FAILURE
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Failed with result 'exit-code'.

 Nov 19 19:01:57 bazzite systemd[2603]: Started app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service - Protontricks.
Nov 19 19:01:57 bazzite flatpak[36337]: bwrap: Can't mkdir /usr/lib/extensions/vulkan: Read-only file system
Nov 19 19:01:57 bazzite flatpak[36332]: error: ldconfig failed, exit status 256
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Main process exited, code=exited, status=1/FAILURE
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Failed with result 'exit-code'.

Flatpak permission issues

ujust upgrade

ujust upgrade

). I've tried researching with no luck, I might have to wipe and install bazzite again but I hope I don't have to go that route.

Here's an example where protontricks fails to run:

 Nov 19 19:01:57 bazzite systemd[2603]: Started app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service - Protontricks.
Nov 19 19:01:57 bazzite flatpak[36337]: bwrap: Can't mkdir /usr/lib/extensions/vulkan: Read-only file system
Nov 19 19:01:57 bazzite flatpak[36332]: error: ldconfig failed, exit status 256
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Main process exited, code=exited, status=1/FAILURE
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Failed with result 'exit-code'.

 Nov 19 19:01:57 bazzite systemd[2603]: Started app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service - Protontricks.
Nov 19 19:01:57 bazzite flatpak[36337]: bwrap: Can't mkdir /usr/lib/extensions/vulkan: Read-only file system
Nov 19 19:01:57 bazzite flatpak[36332]: error: ldconfig failed, exit status 256
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Main process exited, code=exited, status=1/FAILURE
Nov 19 19:01:57 bazzite systemd[2603]: app-com.github.Matoking.protontricks@d4ef2dd0cb9d47dfbba376868b1f2061.service: Failed with result 'exit-code'.

Flatpak permission issues

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