If you haven't read all of Noah Shachtman and Spencer Ackerman's analysis of the virulently bigoted anti-Muslem study materials, the nickel tour is that they were proposing to kill or forcably convert most of the Moslems in the world.
It was attempted when Milosevic and Karadzic tried it on a smaller scale in the Balkans, and their language was far more circumspect than what was in the training manuals:
This is clearly an explicit call for genocide:
For the better part of the last decade, a small cabal of self-anointed counterterrorism experts has been working its way through the U.S. military, intelligence and law enforcement communities, trying to convince whoever it could that America’s real terrorist enemy wasn’t al-Qaida — but the Islamic faith itself. In his course, Dooley brought in these anti-Muslim demagogues as guest lecturers. And he took their argument to its final, ugly conclusion.
“We have now come to understand that there is no such thing as ‘moderate Islam,’” Dooley noted in a July 2011 presentation (.pdf), which concluded with a suggested manifesto to America’s enemies. “It is therefore time for the United States to make our true intentions clear. This barbaric ideology will no longer be tolerated. Islam must change or we will facilitate its self-destruction.”
Great shades of Elvis.
One of the things that the folks at Danger Room neglect to mention is that this is more than bigotry, it is an incitement to genocide that is just as explicit as that of the management of Radio Rwanda RTLM, who were convicted by the ICC.