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After copying my files from my old home folder to the new one, the applications menu is now missing categories, and not displaying all installed applications. Is there a config file I should delete somewhere/a way of resetting the applications menu?

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GNOME application categories are stored in /usr/share/desktop-directories/ and in /home/[your-username]/.local/share/desktop-directories/. Try copying the contents of these folders from your old installation to the new one, and see if it helps.

More info on categories available here.

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