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I have the Numix-Square icon theme installed and in use. Sadly, this comes with the downside that icons that are missing from that icon theme do not use the fallback, hicolor, but show as missing instead.

I found something interesting, though: Every time I use some native UIs, like the Gnome file chooser, it gives me this warning (here with Kate):

(kate:25590): Gtk-WARNING **: 15:51:09.201: Theme file for hicolor has no directories

(kate:25590): Gtk-WARNING **: 15:51:09.201: Theme file for hicolor has no directories

(kate:25590): Gtk-WARNING **: 15:51:09.201: Theme file for hicolor has no directories

So I had a look at it, and indeed, the file /usr/share/icons/hicolor/index.theme was almost empty (just the bare minimum declaration) and thus missing the Directories property. So I downloaded hicolor from freedesktop.org and installed it back. Now it is 55kB large and Directories= is followed by a large list of file paths. I rebuilt the icon cache and restarted Gnome, but the warning is still there and the icons are still missing.

Other icon themes do not use the fallback hicolor neither, but when I select hicolor as my main icon theme everything works fine (but the warning remains).

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