Smudge index entries on first write (too), as well when reading

That happens when the index and a new file is created within the same
second and becomes a problem if we then modify the newly created file
within the same second after adding it to the index. Without smudging
JGit will, on later reads, think the file is unchanged.

The accompanying test passed with the smuding on read.

Change-Id: I4dfecf5c93993ef690e7f0dddb3f3e6125daae15