I'm trying to ascertain how exactly Clara was able to right every wrong the GI imposed on the Doctor's timeline upon entering it. It's easy to digest the GI corrupting the Doctor's timeline with his vast knowledge and previous history with the Doctor spanning back to the Doctor's 2nd incarnation. All we see Clara do is walk into the Doctor's timestream and somehow that miraculously fixes everything.
How did flying the Pandorica into the burning TARDIS cause the Doctor to close the cracks in the universe? Clara saving the Doctor throughout his timeline is the same problem. We see characters do something, we're told that what they do is important, but we don't understand how what they do achieves what we're told. It's the way Moffat's Who
works -- it's magic. *shrug*