Fixing Git commit, as far as it should work as git commit -a.

In order to maintain the same behavior between mercurial and git, the commit should do a "git commit -a" but it was not.

I thought in implement it as optional, but mercurial does not have an index, so I've had to implement one for it and I think it is too much work right now.

So, now it works as documentation said it should.
Good approach, but `status` is probably a bitmasked integer, maybe it's enough to check:

    if not status & pygit2.GIT_STATUS_IGNORED:
        self._repository.index.add(filename)

And probably it worths to add a test for this case.