Update working tree files fully atomically

This avoids commit churn by the assistant when eg,
replacing a file with a symlink.

But, just as importantly, it prevents the working tree being left with a
deleted file if git-annex, or perhaps the whole system, crashes at the
wrong time.

(It also probably avoids confusing displays in file managers.)

Annex/Link.hs

@@ -60,7 +60,9 @@ getAnnexLinkTarget file = do
  -}
 makeAnnexLink :: LinkTarget -> FilePath -> Annex ()
 makeAnnexLink linktarget file = ifM (coreSymlinks <$> Annex.getGitConfig)
-	( liftIO $ createSymbolicLink linktarget file
+	( liftIO $ do
+		void $ tryIO $ removeFile file
+		createSymbolicLink linktarget file
 	, liftIO $ writeFile file linktarget
 	)