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graeme_p - 11:56 am on Sep 15, 2012 (gmt 0)
Apparmour would help there as well: only the config files of the application that was compromised could be changed if you have a restrictive apparmour profile.
Ideally, any application connecting to the network, or dealing with data that might carry malware would not be able to edit its own config files: implementing that would either mean going back to editing config files manually, or a huge effort to create a universal config GUI...
....and it seems a much harder exploit to me than the .desktop file one - except in the case of applications that locally install extensions (especially web browsers).