Wow, excellent episode - this is the way they should all be! Once again, Moffat does not disappoint.
So, some of my thoughts:
I'm not sure if there's more to it (part of me wouldn't be surprised if there were) but I think that archeologist may simply be a future companion of the Doctor, nothing more - not Jenny, not anyone else with a "special" relationship. That being said, she does definitely have a bond with him, so I guess we'll see how it plays out.
I'm very curious to see how things work out with the little girl as well, along with her role in things. She seems to be directly aware of the library at some times, but other times not - for example, her actions in hitting remote control buttons.
As for Donna, she obviously is not dead. I think this ties into the whole "x people have been saved but there are zero survivors". I think this is along the same lines of the whole Rose prophecy of how she would "die in battle" when in fact she did not. Something interfered with Martha's transportation and as opposed to killing her, perhaps she was teleported to this alternate universe or whatever it is in which the girl resides. In other words, people who are saved are in fact saved, but are moved from one universe/dimension/reality to another, hence being considered "dead" in their native environment. So, if this is the case, does that mean Donna is now in the same place as Rose? 😱 😉 😀
Really looking forward to part 2 next week!