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After upgrading from 13.04 to 13.10 my Gnome menu (as in classic-menu-indicator) is missing all my customized entries. The .desktop files are all still in .local/share/applications but the metadata to integrate them into the menu seems to be missing. So my questions

a) Where is the metadata defining the menu structure and entries kept?

b) How can I integrate my existing .desktop files into the menu

I'd be grateful for any help.

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I found the answer myself with the help of the freedesktop.org spec

There was a gnome-applications.menu in ~/.config/menus and as the env variable XDG_MENU_PREFIX was set to "gnome-" the gnome-version trumped my applications.menu.

Renaming my applications.menu to gnome-applications.menu solved the problem

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