We saw the young doctor in a barn.
We have just been told he was once a girl.

So, what is the reincarnation count now?

He wasn't, it was a lie. Missy said so.

One of the statements was a lie, Three guesses which one is most probably the lie.

Hopefully that was Missy's lie

You may have over-analysed it. It's pretty clear that it was the 'lie' that Missy said at the end of that line and is just Moffat poking fun at the discussion of whether there should be a female Doctor.

Since when have you cared about The Doctor?

- Since the Cloister Wars?
- Since the night he stole the moon and the President's wife?
- Since he was a little girl?

One of those is a lie.

The scene served as a decent reminder though that Time Lords aren't humans and aren't bound to the same rules as humans.

That was in no way confirmed as a statement. it was a little joke which was pretty much confirmed as a lie.

No. He could not have been.
In Time of the Doctor, Moffat accounted for all 12 regenerations so he could explain why he was writing the story where the Doctor gets a new regeneration cycle. William Hartnell's Doctor has to have been the First Doctor so unless Hartnell's Doctor was secretly a woman, then it's impossible for the Doctor to have ever been a woman.

Tell that to Caitlin Jenner.

This is such fan invented nonsense. Its not impossible. If the writers write it then its happened. If they decided to write the doctor as turning blue and living the rest of his life as papa smurf it would be possible because they put it in the script.

OP should pay more attention to the dialogue.

Obviously just Moffat messing with the fans for his own amusement. He knows he can't just put that line in there because some people would melt down so he adds the get out clause. Of course his intent could entirely be that the first or second statements were the lie.

The author doesn't even have 'intent' in that sense. The writer's thoughts, feelings, opinions, vices, charity donations, whatever have no relevance whatsoever to the text. We have hundreds of years of literary criticism and none of it necessarily bears any connection to the original writer's intention. Shakespeare's opinions on Macbeth are no more relevant than anyone else's.

It doesn't matter if Moffat imagines the Doctor to have once been a little girl. Contrary to popular belief the writer isn't 'God', the individual reader (viewer in this instance) is. The writer of course understands this, and doesn't necessarily have a dogmatic sense of canon like the viewer does. The writer doesn't think like the audience, he, by necessity, thinks above the audience; anticipating all of the potential responses and desires of that audience and attempting to create something to play to that to create emotional or intellectual response.

Some people, usually when they have very little active experience in creative arts, take this for arrogance but believe me you cannot create if you don't have this sensibility. Goodness me, an author who is worried about every single person's opinion or feelings and lacks the self-belief to implement his ideas and see value in his own thoughts; what would such an author write? The answer of course is: nothing.

It gets my back up when I hear 'arrogant' criticisms of any author because it's so ignorant of what writing entails. The author doesn't respect you, it's true. He can't. Because if he respects you then your viewpoint is as valid as his own and how then can he know what to write if it conflicts in any way? How can he think to manipulate your thoughts and emotions (which is his job) if he has too high a regard for you?

Writers do not think like the audience. To the writer, none of what they write is 'true' or definitive because they made it up. Steven Moffat does not have a definitive opinion on whether the Doctor was once a little girl, I guarantee you. All he had was the knowledge of what the different reactions to that would be from the audience and then the conviction to decide enough people would find enjoyment in the line, from whatever impulse, to include it in the script. Whether it was one of the lies I doubt he's spent a second's thought on. They're all lies to him: he made them up.

I'm diverging wildly from the topic now but I'd recommend the book 'If On a Winter's Night A Traveller...' by Italo Calvino to anyone interested in how the writer's mentality differs from the reader's.

The architecht doesn't live in the blueprints he drew up and neither does the writer.

Ha ha but in all fairness they won't as that would be a step too far. They aren't going to pee off fans to that extent by inventing a whole new regeneration cycle again before Hartnell's Doctor.
Creating the War Doctor was difficult enough for a lot of people to get there heads round, it would be overload and overkill and also unnecessary.
Having the Doctor regenerating into a woman next time or in the future, like the Master/Missy would be enough for people to coap with.

Yes he does. The audience may not agree. The writer may not care that their interpretation is different from his or he may get angry at the idea (I've seen writers feel both ways). But he knows what he actually meant by the lines that he wrote. Author intent entirely exists.

That doesn't necessarily make a difference to the show but Moffat absolutely could have meant that in his view the Doctor was once female.

The tone in missy said it in sounded teasy and joking like