Pattern-based exceptions in .gitignore not working

Example case:

```
*.data
!dont_ignore/*.data
```

Then add a couple files in the workdir: `foo.data` and `dont_ignore/bar.data`.

`git_diff_index_to_workdir()` will correctly ignore `foo.data` but incorrectly also ignore `dont_ignore/bar.data`.

Note that the `.gitignore` file is working as expected when testing with `git status --ignored`.
