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

doc/bugs/add_overwrite_race.mdwn

@@ -50,8 +50,10 @@ added to the annex after all. Test case for this:
 	git-annex add
 	git diff --cached 1
 
-Unsure how to fix this case yet? Maybe it needs to cache the inode,
+Guess it needs to cache the inode,
 hash the file content, then verifiy the inode did not change during
 hashing, and then also use update-index.
 
+> [[done]]
+
 --[[Joey]]