DISCLAIMER: Nothing you recognize is mine. I own only my own theories behind Clara's existence.
This is my first attempt to write in this universe. Please let me know what you think! This is intended as a one-shot, but I reserve the right to come back and make a chapter story out of it if inspiration hits.
The soft whoosh of the T.A.R.D.I.S. engines filled the room moments before she materialized. He had come back. He always did, on occasion, to fill her in on his adventures, tell her stories, ever since she became trapped in the library. Even as he saw her living self more and more often, as their timelines danced and intertwined, still he came back here. They would compare notes, sort out where they had crossed again, until inevitably she would have to smile that soft half-smile and tell him, "Spoilers!" She had long ago digitalized the information in her diary, so that when he came to visit, she could easily fill in the details from his perspective as they talked.
The shadows knew him by now, left him alone. Sometimes the children in the database would join them, sitting enraptured as the two of them regaled them with stories of their adventures. Other times they would sit, just the two of them, as he sobbed over another companion lost, yet another innocent bystander he just couldn't save. Together they would log the details, filing away every aspect of that person as he knew them in the Library's information core. This always seemed to soothe him, knowing that there was that one tiny piece of them he could save, much as he had River herself.
After he met Clara for the third time, he would spend days on end at the Library between his trips with his latest companion. The puzzle of her had put a new energy in him, given him something to focus on besides his loneliness. River had to think fast, as she knew she could only let him find information that wouldn't cause a paradox if he knew it too soon. And steeling herself for the moment she heard the words she knew were coming. She knew the day was fast approaching when their timelines, her past and his future, would part ways for the final time. She would have to tell him the final key to Clara's existence, and then the pair would either cope or they wouldn't. She had no way of knowing which way it would go, it was a fixed point not yet established.
Then the day came that he stepped through those blue doors, determination and guilt warring on his face, and she knew. The moment she stepped forward to embrace him, and he held himself stiff before collapsing in her arms, sobbing. He spoke of Trenzalore, and of facing the horror he thought he'd left behind so long ago. And the moment he had realized…
"River, I love her." Trying to reconcile that with his love and affection for River resulted in the words being spoken in a whisper that broke all three of their collective hearts.
Now she could tell him. How Clara was the daughter of Rose and the human-Time Lord metacrisis version of his earlier incarnation. How she had fallen through a crack in space and time, forever separated from her parents. How that small piece of T.A.R.D.I.S. coral he had given them had been a favorite plaything, over time infusing her with just enough vortex energy to afford her some bit of protection. It was how she had survived stepping into his timelime at Trenzalore. And why the T.A.R.D.I.S. disliked her so, thinking she was a paradox event to itself.
Oh, that didn't go over well. He looked at her in horror, stumbling back. A single tear rolled down her face as he hurried back into his ship and shut the door, not even saying goodbye in his haste. He always said goodbye. Tears turned to sobs as the sounds of the engines faded, both sounds echoing amongst the shelves. Silence returned as she dematerialized back into the database. She was all out of spoilers now, knowing only that he would return to visit her on occasion, one more time at least. She only hoped he would come to terms with the information she had given him, not let it hold him back from the love he so desperately needed to keep him sane. She hoped he would have learned from the past, and not do something stupid before he let his impossible girl back into his life where she belonged.
She really had been born to save him, just as her mother before her had been. And he would need her at his side to weather the storm that was coming. The happenings at Trenzalor had unlocked the doors for the true final battle, he needed his lifeline.