1) making someone aware but saying right away that it's fine (that's what IBM as a self-declared friend and protector of open source should have done in this context)
2) making someone aware and offering a license deal on fair, reasonable and non-discriminatory (FRAND) terms; that would have made sense in this case, too, since TurboHercules stated in its first letter that it wanted to reach an agreement with IBM on such terms
3) making someone aware while simultaneously pursuing exclusionary, anticompetitive objectives
I like the first possibility, I can accept the second one if the offered terms are truly FRAND, but I despise the third option.
4) making someone aware and giving them the opportunity to cease and desist from commercial infringing activity
Is that a threat?
It's one thing to tolerate infringement from a community open-source project. It's another thing to let someone commercialize that technology and bundle it with hardware when a fully proprietary competitor would reasonably expect to be sued in to bankruptcy in no time flat. Should the fact that part of your business is "open" give the whole business immunity from patent infringement claims?
Also, IBM isn't "a self-declared friend and protector of open source". They only made a limited non-aggression pledge. They aren't (and aren't trying to be) in the same category as the FSF and EFF, or even RedHat.
Similarly, your distinction between a "community open-source project" and someone bundling it with hardware makes no sense. Companies bundling open source software with hardware or commercializing it in other ways are simply part of the community as long as they comply with open source terms.
I hadn't really picked up a strong "they're all wrong" vibe from what I've seen of your coverage of the smartphone mess.
You previously just phrased my 3rd option differently to artifically create a 4th option.
Now you don't take into account that I explained 3 different approaches: grant a free license, grant a FRAND license, and prohibit any implementation of the patented invention only to foreclose competition, which is exactly what IBM (a monopolist in the context we're discussing) tried. Fortunately, the European Commission is investigating IBM for suspected violations of EU competition law.
Further, IBM's decade of tolerating Hercules development suggests that they do see a difference between community infringement and commercial infringement.
Your second paragraph doesn't make sense to me given that the patents asserted by IBM in that correspondence were related to the Hercules open source emulator, not specific to any commercial offering. The maintainer of the Hercules project explained on his blog why this was an attack on the Hercules project as a whole: http://ibmvshercules.com/