http://bugs.winehq.org/show_bug.cgi?id=32699
--- Comment #5 from Marco Trevisan (Treviño) mail@3v1n0.net 2013-05-28 13:24:28 CDT --- (In reply to comment #2)
Anything running under any runtime or custom loader (Java, Mono, Python, Perl, Ruby, even running an application with strace or gdb) will exhibit exactly the same stacking problem. Wow the Linux desktop is really owning.
That's not completely true as all these environments are generally able to be launched using an exec that matches the desktop-id or the WMClass or either to provide their WMClass. Also, at least in unity, we have a whitelist of loaders that receive a different treatment (we handle the parameter instead of the launched binary), but this is not something that can be done easily also with Wine if we want to have some basic application <-> desktop-file matching.
However, having a StartupWMClass that matches the launched .exe file (if possibile) would be enough (at least for Ubuntu unity) to properly match wine applications.