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There are applications icons missing in my Gnome-Shell 3.8.2 overview, but this wasn't like that on a fresh install with Gnome3-PPA enabled. I do not have or had the Gnome3-Staging-PPA enabled.

I had Alacarte installed, as I conveniently wanted to edit the icons showing up in the overview. Unfortunately, it messed up and placed all newly installed applications to the "other" category, so I purged it.

Also, I tried the Pantheon File Manager, just to have a look at the miller columns. Purged as well, but maybe there is some configuration file messed up?

At the moment, I have the Faience icon theme installed, but setting a different icon theme in Tweak Tool does not change anything.

Whenever I install a new application, the icon won't shop up in the overview. Is there a way to 'clear' my messed up configuration? I really do not want to edit every single .desktop-file manually. Menulibre is currently installed on my system, but changing the icons manually does not make them show up in the overview.

Screenshot

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If you create a temporary account or use the guest account, the icons appear correctly there? Check you don't have modified versions of those launchers in ~/.local/share/applications. –  Salem Jun 17 '13 at 20:53
    
I have checked on a different unser account, but the icons are gone there too. The local/share/applications folder shows some weird .desktop-files, as some of them contain the line hidden=true (gimp or totem for instance), but none of the not showing icons. –  leonis_csem Jun 18 '13 at 10:46
    
I checked the *.desktop entries and it seems that only those icons get affected, which are not located in the /usr/share/icons directory but in a separate directory as it is the case for xdiagnose. –  leonis_csem Jun 22 '13 at 13:04
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