The same problem microsoft was facing when they introduced windows 7. They
developed a solution (AppUserModelIDs) which maps quite cleanly to the linux
solution (WMClass). We just need to implement that AppUserModelID stuff and
export it as WM Classes.
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This bug is a huge usability problem nowadays (in both Gnome Shell and Unity).
The current solution matches all wine applications to a single desktop file,
because every wine window has a WM_CLASS of "Wine" and the desktop file a
StartupWMClass=Wine . I'd consider this incorrect, because
* Every