In order to avoid racy-git, we zero out the file size for entries with
the same timestamp as the index (or during the initial checkout). This
is the case in a couple of crlf tests, as the code is fast enough to do
everything in the same second.

As we know that we do not perform the modification just after writing
out the index, which is what this is designed to work around, tick the
mtime of the index file such that it doesn't agree with the files
anymore, and we do not zero out these entries.