upgrade: Handle upgrade to v6 when the repository already contains v6 unlocked files whose content is already present.

Closes https://github.com/datalad/datalad/issues/1020

The use of runWriter in scanUnlockedFiles broke due to this change;
it failed with blocked indefinitely in mvar, because the database write
handle was taken while linkFromAnnex needed to also write to it (to update
the inode cache). So, switched to using a separate runWriter for each call
to addAssociatedFileFast. A little less efficient, but not greatly; the
writes should all still be cached.

Annex/WorkTree.hs

@@ -11,7 +11,10 @@ import Annex.Common
 import Annex.Link
 import Annex.CatFile
 import Annex.Version
+import Annex.Content
+import Annex.ReplaceFile
 import Config
+import Git.FilePath
 import qualified Git.Ref
 import qualified Git.Branch
 import qualified Git.LsTree
@@ -54,24 +57,37 @@ ifAnnexed file yes no = maybe no yes =<< lookupFile file
  - This is expensive, and so normally the associated files are updated
  - incrementally when changes are noticed. So, this only needs to be done
  - when initializing/upgrading a v6 mode repository.
+ -
+ - Also, the content for the unlocked file may already be present as
+ - an annex object. If so, make the unlocked file use that content.
  -}
 scanUnlockedFiles :: Annex ()
-scanUnlockedFiles = whenM (isJust <$> inRepo Git.Branch.current) $ 
-	Database.Keys.runWriter $ \h -> do
-		showSideAction "scanning for unlocked files"
-		liftIO $ Database.Keys.SQL.dropAllAssociatedFiles h
-		(l, cleanup) <- inRepo $ Git.LsTree.lsTree Git.Ref.headRef
-		forM_ l $ \i -> 
-			when (isregfile i) $
-				maybe noop (add h i)
-					=<< catKey (Git.LsTree.sha i)
-		liftIO $ void cleanup
+scanUnlockedFiles = whenM (isJust <$> inRepo Git.Branch.current) $ do
+	showSideAction "scanning for unlocked files"
+	Database.Keys.runWriter $
+		liftIO . Database.Keys.SQL.dropAllAssociatedFiles
+	(l, cleanup) <- inRepo $ Git.LsTree.lsTree Git.Ref.headRef
+	forM_ l $ \i -> 
+		when (isregfile i) $
+			maybe noop (add i)
+				=<< catKey (Git.LsTree.sha i)
+	liftIO $ void cleanup
   where
 	isregfile i = case Git.Types.toBlobType (Git.LsTree.mode i) of
 		Just Git.Types.FileBlob -> True
 		Just Git.Types.ExecutableBlob -> True
 		_ -> False
-	add h i k = liftIO $ Database.Keys.SQL.addAssociatedFileFast 
-		(toIKey k)
-		(Git.LsTree.file i)
-		h
+	add i k = do
+		let tf = Git.LsTree.file i
+		Database.Keys.runWriter $
+			liftIO . Database.Keys.SQL.addAssociatedFileFast (toIKey k) tf
+		whenM (inAnnex k) $ do
+			f <- fromRepo $ fromTopFilePath tf
+			destmode <- liftIO $ catchMaybeIO $ fileMode <$> getFileStatus f
+			replaceFile f $ \tmp -> do
+				r <- linkFromAnnex k tmp destmode
+				case r of
+					LinkAnnexOk -> return ()
+					LinkAnnexNoop -> return ()
+					LinkAnnexFailed -> liftIO $
+						writePointerFile tmp k destmode