Third, it is also clear that we still really have no proper clue as to just who (or what) Clara Oswald really is. She was a Dalek once - more faulty technoology, a Victorian governess come Torchwood associate, and once more a school teacher in 21st C London. She has already been dead twice and yet seems to have the endurance of the Energizer rabbit - or a Time Lord. I vote she's really the Rani.
You obviously missed the "Name of the Doctor"
where the Great Intelligence jumps into the wound in time at the heart of the Doctor's Tomb - his abandoned Tardis from after his death - in order to rewrite the Doctor's History turning every victory into defeat. Clara then also jumps into the wound and is split into multiple versions scattered throughout the Doctor's timeline each dedicated to helping the Doctor and countering the effects of the Great Intelligence.