fix overwrite race with small file that got large

fix overwrite race with small file that got large

When adding a small file, it does not get locked down, so can be modified
after git-annex checks that it's small. The use of queued git add made the
race window nice and wide too.

Fixed by checking if the file has changed, and by not using git add.
Instead, have to recapitulate git add's handling of things like symlinks
and executable files.

Sponsored-by: Jochen Bartl on Patreon