Re: TARDIS and Clara - over at lj someone pointed out to me the TARDIS might have been preemptively blaming Clara for events from Journey into the Centre of the TARDIS and didn't anymore once that was done with, but I can't remember anything about that episode other than the image of a burned person moving, so I couldn't say. Anyway, you're probably right about the TARDIS not knowing about the fragments of Clara before Trenzalore (or Simeon's fragments, of course), but afterwards would.
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Re: TARDIS and Clara - over at lj someone pointed out to me the TARDIS might have been preemptively blaming Clara for events from Journey into the Centre of the TARDIS and didn't anymore once that was done with, but I can't remember anything about that episode other than the image of a burned person moving, so I couldn't say. Anyway, you're probably right about the TARDIS not knowing about the fragments of Clara before Trenzalore (or Simeon's fragments, of course), but afterwards would.