git-apply: actually apply patches and update the index

git-apply: actually apply patches and update the index

We update the index only if the "--index" flag is given,
so you can actually use this as a strange kind of "patch"
program even for non-git usage. Not that you'd likely
want to, but it comes in handy for testing.

This _should_ more or less get everythign right, but as
usual I leave the testing to the usrs..