40250 issues (broke/missing apps)

Version on server (40250) is not newer than system version (40250)
6.5.9-1373.native #1 SMP Wed Oct 25 03:45:34 PDT 2023 x86_64 GNU/Linux
KDE 5.27.9
Qt 5.15.2
X11

Kwrite is gone, so is every other note related app

Steam won’t launch via flatpak or thirparty bundled (Conty) packages:

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: iris
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: iris
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast

I have a similar issue on Gnome X11.
When playing sudoku the widgets get stuck.
This is what is logged in the journal:

Oct 28 02:49:51 clear2 org.gnome.Sudoku[10413]: libGL error: failed to load driver: iris
Oct 28 02:49:51 clear2 org.gnome.Sudoku[10413]: libGL error: failed to open /dev/dri/card0: No such file or directory
Oct 28 02:49:51 clear2 org.gnome.Sudoku[10413]: libGL error: failed to load driver: iris
Oct 28 02:49:51 clear2 org.gnome.Sudoku[10413]: libGL error: No matching fbConfigs or visuals found
Oct 28 02:49:51 clear2 org.gnome.Sudoku[10413]: libGL error: failed to load driver: swrast
Oct 28 02:49:51 clear2 gnome-sudoku[10413]: Failed to realize renderer of type ‘GskGLRenderer’ for surface ‘GdkX11Toplevel’: Unable to create a GL context
Oct 28 02:49:51 clear2 gnome-shell[1364]: Window manager warning: Buggy client sent a _NET_ACTIVE_WINDOW message with a timestamp of 0 for 0x2400007
Oct 28 02:49:51 clear2 gnome-sudoku[10413]: GtkBox 0x5626740628f0 exceeds SudokuWindow size: requested 350×154 px, 349×32 px available
Oct 28 02:49:53 clear2 gnome-sudoku[10413]: GtkBox 0x5626740628f0 exceeds SudokuWindow size: requested 413×110 px, 349×32 px available
Oct 28 02:50:08 clear2 gnome-sudoku[10413]: Failed to realize renderer of type ‘GskGLRenderer’ for surface ‘GdkX11Popup’: Unable to create a GL context

Sudoku works fine on Gnome Wayland, but in that environment the icons for flatpak applications do not show. They can still be launched via terminal ( flatpak run application ) so not a blocking issue, but another effect with this issue is that the flatpak applications cannot be selected as default apps or are available as ‘open with’ option. This is inconvenient as I like to have flatpak VLC as default app for playing videos.

Clear Linux OS minimizes the customizations and patches in support of the desktop and provides a generic GNOME implementation.