Pull example doesn't fully update the index #389

Following the pull example and doing a simple fast-forward pull you'll get the inverse of what was changed in your working directory.

Repo Steps

1. Checkout out the pull-example-dirty-index branch
2. npm install && ./test.sh && cd downstream && git status
3. Notice that there is 1 deletion. I.e. the index isn't properly updated.

Doing a nodegit.Checkout.head doesn't update the index either.

Possibly related pygit2 stack overflow question

Originally reported by @ubercow