So who is the Ruth Clayton Doctor?

Theories 

1. She is a different universe Dr

2. She is the Doctor from season 6B. There is a regeneration between 2 and 3, which we did not see. 

Hence she is working for the CIA. Celestial intervention agency

3. She is the Valeyard. Which would put her in Dr's past

3. She is a pre-Hartnel Dr, the Morbius Doctors are canon. It was her coat in the control room

4. There was something going on, she is the Doctor from the past....But there were looms or something.

5. She is the Peter Cushing Doctor regenerated

Update

Chibnal says she is not a clone