UPDATE: We found a better fix for that and we integrated it into TROMjaro by default. See this.
The new libadwaita approach to the Gnome themes is breaking the design for any custom theme that you have on your system. This means if you have a dark theme with 3 buttons on the left side of the window, in your preferred order, any app that migrated to the new libadwaita will not care about these and they may have a light theme with just one button on the right side of the window.
I consider this a bug that needs to be fixed. For now we have found a manual fix to the issue.
If you see any particular app that does not respect your system’s theme, and this app is not flatpak, plus this app seems to be a “gnome” one, like Gnome Calculator, Gnome Maps, and the like, then from the menu or app finder, right click it then edit. You should see something like this:
In the Command section, instead of touche in our example, add this entire thing:
sh -c 'env GTK_THEME="$(xfconf-query -c xsettings -p /Net/ThemeName /l)" touche'
This forces this particular app to use your current system theme. Note in the above code that you need to replace touche with whatever command your app has.
Save. Done.
Maybe in the future we can automate this, but for now this is how you can do it…
It is outrageous that the Gnome team is breaking this bond between the system and apps. The apps should always respect the system’s settings, else everything becomes a huge mess.