Comment 26 for bug 635223

As the writer of winemenubuilder, the part of Wine that builds freedesktop menus, I have this to add.

The menu structure is driven by the per-shortcut .menu files under ~/.config/menus/applications-merged. The .directory files in ~/.local/share/desktop-directories and the .desktop files in ~/.local/share/applications/wine/... are referenced from the .menu file to describe and thumbnail the subdirectories and shortcut. Thus the .menu file is crucial, it is what places the icon in the right place, and it is the absence of the .menu file that causes the .desktop entry to appears under "Other" in Gnome. If you want to build a single flat menu structure without subdirectories, good luck: most uninstallers for Windows applications are all named "Uninstall". Mint 8 tried the single flat menu idea and it didn't work that well for Wine.

The poorly researched "desktop-id" idea is, in my understanding, fundamentally broken and will regress not only Wine but Java and any other framework that launches through a layer of indirection (eg. .desktop file launched "java -jar ..." or "/bin/sh ...", which then starts the real application).