With a fair bit of fan speculation that Clara is possibly CAL, perhaps when she said "run, you clever boy" it has an alternative meaning

Does anyone think that maybe its not a statement but more for something that the Doctor should do in association with a computer. Could a program be called "You Clever Boy" and Clara is to tell the Doctor to 'run' it ?

Sometimes Moffat gives us a hint and it can be something as plain as that.

Interesting idea. Not saying I like it or think it's "correct" but I like the lateral thinking behind it.

On a similar tack, when someone says "run", they might be giving a "command" or making a "threat" rather than offering a "helpful suggestion" - like someone pointing a gun, saying "run" and starting to count backwards from ten - they wouldn't be saying "run" to help you.

who's CAL?

I think the Run You Clever Boy thing is a bit of a stretch, but it's not impossible that CAL is another incarnation of Clara.

Or perhaps the Doctor's been in the alternate reality of the Library since Series 4, and the Doctor is seeing Clara all over the place in the same way that Donna finally spotted that all the children were the same...

Not until Miss Evangelista pointed it out to her she didn't.

Indeed. But still, the Doctor could have been surrounded by Claras through his life and not put two-and-two together until now.

What if Clara has already been a companion and neither of them remember it? I know that people's first thought when Oswin was introduced in Asylum that she might have been a future companion that isn't giving anything away, but what if it's more linear than that?

Are the events that brought her tenure to a close the reason the TARDIS has a thing against her?

So does everyone know who Clara is except The Doctor?
When she fiddled with The Dalek records of The Doctor, did she somehow make herself the Dalek's enemy and that was why she was in that room in AOTD.
If so, The Doctor might need to change it back to make sure Clara is ok and just an ordinary girl.

Even accounting for possible timey-wimeyness, that would mean that the Daleks chose to imprison her for being an enemy of the Daleks before she re-wrote their databanks.

I have been backing this idea for a while.

You can add too that 'remember' becomes 'save' in computer language.

So it is

RUN: YOU CLEVER BOY
SAVE

At which point the program (clara) terminates.

Oh yes it said that on the painting in the Bells of St John episode

Would the Daleks know of what was going to happen beforehand or did Clara/Oswin swap places with The Doctor?

There have been at least three others on here who have posited that theory, some from before the new series started.

I don't give it much credence myself, but it would be suitably twisty!

Till she's loaded up again? This makes so much sense.