Steven Moffat has insisted that he is not changing the numbering of the Doctors. He makes it clear that John Hurt’s “War Doctor” (as revealed in The Night of the Doctor) doesn’t alter anything.
Moffat explains in the new issue of DWM,: “I’ve been really, really quite careful about the numbering of the Doctors. He’s very specific, the John Hurt Doctor, that he doesn’t take the name of the Doctor. He doesn’t call himself that. He’s the same Time Lord, the same being as the Doctors either side of him, but he’s the one who says, ‘I’m not the Doctor.’ So the Eleventh Doctor is still the Eleventh Doctor, the Tenth Doctor is still the Tenth…
He adds: “Technically, if you really counted it, the David Tennant Doctor is two Doctors, on account of the Meta-Crisis Doctor [in Journey's End]… It’s not a matter of counting the regenerations, but of counting the faces of the Time Lord that calls himself the Doctor. There’s an anomaly Doctor slotted in somewhere, that’s all. In the script to The Day of the Doctor, Matt’s Doctor was called the Eleventh, and David’s was called the Tenth, so the numbering stays exactly the same – and we call Peter Capaldi the Twelfth Doctor.”
Everyone seemed confused about this issue, so I thought it'd be a good idea to post the answer. The actual question now is: How many regenerations The Doctor has left, if Moffat says he believes in the 12 regenerations deal?