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

Command/Import.hs

@@ -229,7 +229,8 @@ startLocal o addunlockedmatcher largematcher mode (srcfile, destfile) =
 		-- weakly the same as the originally locked down file's
 		-- inode cache. (Since the file may have been copied,
 		-- its inodes may not be the same.)
-		newcache <- withTSDelta $ liftIO . genInodeCache destfile
+		s <- liftIO $ R.getSymbolicLinkStatus destfile
+		newcache <- withTSDelta $ \d -> liftIO $ toInodeCache d destfile s
 		let unchanged = case (newcache, inodeCache (keySource ld)) of
 			(_, Nothing) -> True
 			(Just newc, Just c) | compareWeak c newc -> True
@@ -250,7 +251,7 @@ startLocal o addunlockedmatcher largematcher mode (srcfile, destfile) =
 				>>= maybe
 					stop
 					(\addedk -> next $ Command.Add.cleanup addedk True)
-			, next $ Command.Add.addSmall (checkGitIgnoreOption o) destfile
+			, next $ Command.Add.addSmall destfile s
 			)
 	notoverwriting why = do
 		warning $ "not overwriting existing " ++ fromRawFilePath destfile ++ " " ++ why