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.
It is not difficult to implement::

```python
for filename, status in status.items():
    if status == pygit2.GIT_STATUS_WT_MODIFIED:
        self._repository.index.add(filename)
    elif status == pygit2.GIT_STATUS_WT_DELETED:
        self._repository.index.remove(filename)
```
But it is failing me. Trying to fix it.