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@makin: the message is obviously automated and I do believe the penalty itself, at least since after penguin, is also automatic.
So you're just disregarding the searchengineland interview with Matt Cutts?That interview is just about any manual penalty for which you received a notice which is supposed to be 100% of the time as of late. I guess I should consider myself lucky that I haven't broken any rules lately since I've never got any notifications other than the "unnatural links" last year. So, these "unnatural links" are not addressed specifically in the interview except in this interesting quote:
... especially after last year’s mess of sending out unnatural link warnings that caused panic, then further confusion, when Google said they could maybe be ignored.