OK, here's what I'm thinking:

We first met Clara in the series 7 episode Asylum of the Daleks. She thought she was just a survivor of a spaceship crash, but by the end of the episode we learn a terrible truth (as does she): she's a human who has become, over a long period of time, a dalek, and there's nothing that can be done for her. It's a genuinely sad episode.

In the latest series 9 episode, Clara was placed inside dalek armor by Missy. When Clara asks Missy how she can get out, Missy dodges the question. Later, when the Doctor finds her in the armor, he says those words you never want to hear from him: "I'm so sorry." It usually indicates that the poop has, in fact, already hit the fan.

We later see Clara and the Doctor together, with her looking like she always had...but then, in the older episode, she thought she was fine and perceived herself as completely human, when in fact she was a dalek.

Long story short...I think we've seen the beginning of Clara's awful transformation. It'll be a most terrible way for the Doctor to have to part with a companion.

I've been watching this season via Microsoft TV and Movies. I used to do all this sort of viewing on Google Play, but I've been becoming increasingly unhappy with both Google and Android. Maybe that could be a topic for GeekSpeak.