I've executed the initial obfuscation run with -useuniqueclassmembernames. When I execute an incremental run with the same option, this works fine on windows and fails on linux systems (in both cases I tried 2 different physical machines).
The problem that occurs on the linux machines is the warning that's created in MappingKeeper#processFieldMapping.
when I remove -useuniqueclassmembernames the incremental run also works on the linux machines.
I also tried this with 4.7 beta 2 which has the same behavior.
My fix is to skip the -useunique... option anyway as I think we don't need it but I'm reporting this issue because of the OS dependent problem which I really don't understand.