test suite passes in direct mode

This fixes a bug with git annex add in direct mode. If some files already
existed in the tree pointing at the same key as a file that was just added,
and their content was not present, add neglected to copy the content to
those files.

I also changed the behavior of moveAnnex slightly: When content is moved
into the annex in direct mode, it does not overwrite any content already
present in direct mode files. That content may be modified after all.

Annex/ReplaceFile.hs

@@ -0,0 +1,35 @@
+{- git-annex file replacing
+ -
+ - Copyright 2013 Joey Hess <joey@kitenet.net>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Annex.ReplaceFile where
+
+import Common.Annex
+import Annex.Perms
+
+{- Replaces a possibly already existing file with a new version, 
+ - atomically, by running an action.
+ - 
+ - The action is passed a temp file, which it can write to, and once
+ - done the temp file is moved into place.
+ -}
+replaceFile :: FilePath -> (FilePath -> Annex ()) -> Annex ()
+replaceFile file a = do
+	tmpdir <- fromRepo gitAnnexTmpDir
+	createAnnexDirectory tmpdir
+	tmpfile <- liftIO $ do
+		(tmpfile, h) <- openTempFileWithDefaultPermissions tmpdir $
+			takeFileName file
+		hClose h
+		return tmpfile
+	a tmpfile
+	liftIO $ do
+		r <- tryIO $ rename tmpfile file
+		case r of
+			Left _ -> do
+				createDirectoryIfMissing True $ parentDir file
+				rename tmpfile file
+			_ -> noop