There are so many theorys about who clara is and what is up with her, but there is something that many people forget. Someone who was also present in different points throughout time and who also knew the doctor! He may have been a bit more exagerated in that he remembered the doctor and was a bit psychic, but same concept. Yep, im talking about this bad boy 

tim latimer. He played a vital part of the story line of human nature, but was also pointed out to have met the doctor in other lives. The doctor said he had abilities because of “an extra synaptic engram.” maybe this is the same with clara.