Fix indices of test repos so that they're not dirty

Although `git diff` returns nothing for those repos, `git status` complains that there are some modified files.

There are great chances that this relates to crlf.

This PRs updates the indices of those repos whith new version where all the "seen-as-modified" files have been staged.

Hopefully this should help #722 move forward, provided Travis is also happy with the proposed changes.

/cc @Therzok @carlosmn