And all this time Clara was a sleep and has no idea who the Doctor is?
Not likely (the second part) - she was cloned when she went to find the child (Sandeep's) father. Also, why Clara in that scenario? That supposes that the Zygons cloned an otherwise unremarkable and unimportant human and then worked to get that person into the Doctor's company and trust. Far, far more sensible to just clone someone already in that position.
One must also remember that these rogue Zygons are apparently a NEW breed and so they have only actually come about (born/hatched/grown/whatever) in the recent past, well after Clara met the Doctor. Unless, of course, they have time travel capabilities but that has not been hinted at and seems unlikely anyway.
Okay, I'm a nerd - it's official.
Biting the hand that feeds IT
