From The Guardian: Chelsea Manning (formerly Bradley) publicly stated that she is a woman, and intends to undergo hormonal replacement therapy. This comes right after her sentence to 35 years in prison.
So I guess this settles the question of why Chelsea Manning was not identifying as transgender. I was never sure if it was because of the court case, because of personal reasons, or because she had decided that she was not mtf after all (instead being one of the many other things in the trans umbrella).
I'm interested to see how the Free Bradley Manning people will react. They march every year in SF pride, because I guess they considered her a hero who was also a gay man. I'm vaguely optimistic that their next action will be to call for a presidential pardon of Chelsea Manning. It could be a good show of trans inclusion in gay activism.
I don't think I really agree with the Free Bradley Manning people. They regard her as a whistleblower, but what did the public actually learn from the leaks? It's not like learning that the NSA is spying on us. Nonetheless, I regard Chelsea with compassion, whether her convictions were just or not.