Is this the NYT's way of calling Obama a liar? If so I wish they had used clearer words. But at least it seems that they are slowly waking up.
http://www.nytimes.com/2013/06/07/opinion/president-obamas-d...
http://gawker.com/the-new-york-times-quietly-softened-its-sc...
So maybe it's a global spying program that just happens to include domestic data.
No, it means that, for reasons best known to themselves, they have now decided that this deserves to be an "issue". This sort of thing has been going on for decades, and the NYT has always had sources inside the government so they have known about it.