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[...] In the long run I would like to integrate it into the SS2Technical FAQ, since the instructions largely overlap and some are not Linux specific.
Running it through Lutris, as sarge945 suggested, does not help; the same issue as above happens.
I'm having the same issue as confused123. On running SS2Tool-v.6.1.1.8.exe, it says "Local game content version is unknown", then deletes most of the executables and data files in the directory, except for SHODAN.DIF and HYDRO2.DIF.Running it through Lutris, as sarge945 suggested, does not help; the same issue as above happens.
sarge945It sucks that @Kolya appears to have disappeared from the forums because SS2Tool is completely broken on Linux, you have a solution, but you can't release it because you need clearance from someone who appears to have been transported to another dimension.