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In the Time of the Doctor context, did she do that by holding on to the outer edge of the TARDIS and travel through time and space that way?
Yes, Clara hung onto the key and outside of the TARDIS. The TARDIS extended a field, I recall the Doctor saying, to protect her.
The TARDIS, did not want Jack Harkness to hang on to it, it tried to throw him off.
Yeap. Well, that's what the Doctor said and what we obviously saw.... Didn't this kill Captain Jack Harkness though when he did it before? The 50th and Christmas special episode destroyed a lot of important things in my opinion.