I'll start off by reiterating what's in my signature: "Disclaimer: not only am I not a lawyer, I'm not your lawyer. Therefore, this does not constitute legal advice." Read it, learn it, love it, live it.
Now, I'm going to go out on a limb here, but, given your repeated insistence that this technique is well-known and widely used, the basis for all sorts of major software, MIT published it, yadda yadda yadda, I find it somewhat difficult to imagine that an examiner would completely miss the paper and/or the fact that it was published in October 2003, totally overlook the technique being used all over the place since then, decide that the technique in the application had never before been contemplated in the history of mankind, tell the patentee that they're geniuses on par with Newton, Einstein, Lemelson, and Hannibal Lecter, and issue them a patent on a silver platter. Examiners may not be "omniscient and clairvoyant" (to borrow a phrase), but they're not total blithering idiots either. In other words, I'm betting that the October 2003 publication has been considered already. I strongly suggest that you read the entire prosecution history, which you've apparently already located in PAIR, and make sure that the October 2003 paper was not already considered by the examiner and already overcome by your competitor's brilliant arguments, otherwise you may be sticking your neck out over the chopping block while handing your competitor a nice sharp axe.
So, precisely because of your assertion that everyone on the planet knows about this technique, I'm guessing that the October 2003 pub isn't a slam-dunk rejection, and that you're probably going to have to argue that publication in combination with something more. Might be doable, but you're going to have to find that "something more" somewhere in public, dated back then so that it "anticipates" (i.e., "comes before") their filing. And even assuming you do, your competitor can still argue that they came up with the idea before that, and they can use their own documentation during reexamination to do what's called "swearing back" or "antedating the reference" (see the USPTO's Manual of Patent Examining Procedure (MPEP) Section 715 for starters).
Next, I'd like to point out that they still have a continuation application in process, and I'd like to reiterate that one of the uses for this is to more precisely tailor patent claims while suing someone.
Returning briefly to your having put so much detail into your posts in this thread, it would be remiss of me not to mention the topic of "willful infringement", which a judge can use to increase the damage award to a plaintiff by up to a factor of three (known as "treble damages" in the vernacular). "Sure, I knew about their patent, but it's invalid because I said so!" is not generally a defense to willful infringement. "But there was an October 2003 publication from MIT!" likewise isn't really all that great of a defense (although it may be "a" defense, a little, sort of -- a jury might buy it, you never know, worth a shot, can't hurt, might be very amusing) if the USPTO already considered that publication during prosecution -- have you read the full history yet (it's available on PAIR, you know) to see if it was?
Now, consider that an infringement lawsuit can be filed at any time. Sure, right now, you're in your apartment typing in your code, and nobody knows about it. So, what happens when you've spent six months finishing your first product, getting your investors lined up, have your website all set for sales, and finally go live and (gulp!) advertise your product for sale? Do you think your competitor won't notice? Won't care? Will give you five years to make gobs of money before deciding to test out that patent in court? Will never try to sue because the patent might be invalid on the basis of an October 2003 publication from MIT so you're free to do whatever you want?
Well, maybe. Maybe not. You won't know until you check your mail. Every single morning.
Now, the situation isn't necessarily that bad. You may be entirely in the clear, not a worry in the world, all just a misunderstanding. But you aren't going to find that out by posting general comments/questions along the lines of "someone published something that was EXACTLY THE SAME in 2003 so their patent must be invalid, right?" on web forums. Not even on web forums inhabited by the greatest minds in intellectual property law. No, the way you find that out is by going to a patent attorney's office, forking over a huge steaming wad of cash sufficient for a downpayment on a nice new car, and asking for an opinion letter.