The Doctor told Clara that she reminded him of a friend who died, to which Clara responded, "well, whoever she was, I'm not her." The friend The Doctor mentioned was a previous version of Clara who died during their time together.
Clara would have wanted nothing more than for the Doctor to be the Doctor again. Her final message to him even is "Run you clever boy, and be a Doctor".
Nonetheless, at this point Clara definitely knew the Doctor's name (be it re-remembered or heard by River), and even though she was probably quite shaken up by traveling in his time stream, some of her conversations with Twelve (though I'm afraid I currently fail at finding one) suggest she still knows quite a lot of ...
Clara is the future child of the Doctor and River who's had her memory erased. The two Time Lords must be up to something on their nights away from River's prison cell.
Both of them had ties to each other since their childhoods — thanks to time travel — and their relationship blossomed as she was the companion of his eleventh and twelfth incarnations. Soon enough, it became clear that Clara and the Doctor were most definitely in love with each other, despite not becoming lovers.
Throughout Doctor Who season 8, Clara had been forced to choose between the two important men in her life, constantly trying to balance her two identities and experience the best of both worlds. Danny's death forced her to recognize that this was no longer possible - and she chose Danny over the Doctor.
At the end of an adventure, an avatar of Bill Potts restores the Doctor's memories of Clara with a mental image of her telling him not to forget her again.
River, who is a professor of archaeology and carries a TARDIS-colour/pattern diary of her adventures, is able to convince the Doctor of his future trust in her by whispering his real name into his ear, which he explains he would only divulge under rare circumstances.
The Doctor loved River Song enough that he suppressed the urge to roam for over two decades. This is something he was never able to do before River, and has never done again since. This proves, definitively, that River Song was not, and never will be, just another companion.
It is a question that was posed to Steven Moffat over a year ago. In answering that question in Doctor Who Magazine, Moffat suggested that the TARDIS' dislike of the current companion may be due to her sceptical nature and how she did not seem suitably awed by the Doctor's spaceship.
Companions like Katarina, Adric, and Kamelion have sacrificed themselves for the Doctor, and their deaths have had a lasting impact on him. Clara, Bill, Astrid, Adelaide, and River have all faced tragic ends but have returned or found ways to continue their adventures in different forms.
In Victorian London, there's “sweet little Clara” from the Rose & Crown, who's also an upright children's governess. In the far-flung future, Oswin Oswald, the shipwrecked Junior Entertainments Manager from Starship Alaska, in reality a human-Dalek conversion refusing to accept her fate.
Behind the scenes. Clara's headstone in 1892 states that she was born on 23 November 1866 and died 24 December 1892, meaning she not only shared the same birth date as Doctor Who itself but that she was also 26 years old when she died.
Plot. Clara phones Danny, ready to admit the full truth of her travelling with the Twelfth Doctor and that she sincerely loves Danny. Danny is killed by a passing car midway through the call. Visibly upset, Clara schemes to use a hypnotic patch on the Doctor to blackmail him into saving Danny.
The woman in the shop who gave Clara the Doctor's number is brought up in "Deep Breath". The Twelfth Doctor remarks it seems as if someone is trying to bring the Doctor and Clara together. The episode "Death in Heaven" reveals it was the Master (as Missy) who gave the number to Clara.
The variations of the Master also know the Doctor's real name, as they grew up together, and Clara, who learned it from the Time-War book, although it is never clarified whether she remembers it in “The Name of the Doctor”.
Truly, madly, deeply. To some, companion Rose Tyler was the greatest love of the Doctor's life. He seemed to have a closer bond with her than almost anyone he'd travelled with before, and as time went on it was increasingly clear that she was deeply in love with him.
To answer the question, no, there's never anything to conclusively state that the Doctor has ever been physically intimate with Rose or with any of his human companions. There also never will be. It's a family show.
River doesn't recognise the Twelfth Doctor as the Doctor because "he has limits", referring to the Time Lords' twelve-regenerations limit first mentioned in The Deadly Assassin (1976).
In this episode, River fails to recognize the Doctor because she has no idea that he managed to gain another regeneration cycle, and no matter what he says or how many blatant hints he keeps dropping to her about his true identity, she keeps missing the forest for the trees.
When Rose absorbed the time vortex into herself, she became a deity that could see all of space and time at once. She scattered the phrase "bad wolf" as a warning for the doctor, both ecclestone and tennant. She chose the words bad wolf because she knew their final meeting would be at bad wolf bay in norway.
Ultimately, the Doctor had to have his memory of Clara wiped to allow her to return to Trap Street and restore the timeline. But not before Clara, in a stolen TARDIS from Gallifrey, flew off with immortal companion Ashildr, for her own adventures in time and space!
Following The Doctor's request, Gallifreyan technology is used to pluck Clara out of her time stream during her final heartbeat on Trap Street. Clara rejoins The Doctor with her body in stasis and they escape to the end of the universe together.
She died in the process but on Clara's urging, the Twelfth Doctor used a Mire repair kit to bring her back to life. The side effect was that she effectively became immortal.
