So I've run into this issue. First of all, the GitHub page seems to indicate that this only affects Windows machines. Is that true? I'm experiencing the problem when doing a fresh clone of a migrated repo on OS X.
Secondly, if I do what is suggested in this fix, I end up modifying thousands of files. The problem is that when I look at the diff of the staged changes it appears to have modified the entire file. My question is: won't this make all diffs of future versions of these files as compared to versions before the commit to fix the line-endings useless?
Forgive me if this is an SVN-specific issue, but in SVN changes like this would mean that the diffs would show the entire file changed whenever you attempted to diff versions that spanned the commit where the line-endings were fixed.