[JoshStrobl]

I ended up putting this in my .gitconfig (global)

    [alias]
        permission-reset = "!git diff -p | grep -E \"^(diff|old mode|new mode)\" | sed -e \"s/^old/NEW/;s/^new/old/;s/^NEW/new/\" | git apply"

So when I run git permission-reset, it sorts it out.