diff --git a/Annex/Ingest.hs b/Annex/Ingest.hs
index 7f38e9beb7..36930baf48 100644
--- a/Annex/Ingest.hs
+++ b/Annex/Ingest.hs
@@ -13,6 +13,7 @@ module Annex.Ingest (
 	ingest,
 	finishIngestDirect,
 	finishIngestUnlocked,
+	cleanOldKeys,
 	addLink,
 	makeLink,
 	restoreFile,
@@ -27,6 +28,7 @@ import Annex.Content.Direct
 import Annex.Perms
 import Annex.Link
 import Annex.MetaData
+import Logs.Location
 import qualified Annex
 import qualified Annex.Queue
 import qualified Database.Keys
@@ -143,6 +145,7 @@ ingest (Just (LockedDown lockingfile source)) = withTSDelta $ \delta -> do
 		-- linkAnnex falls back to copying if a file
 		-- already has a hard link.
 		cleanCruft source
+		cleanOldKeys (keyFilename source) key
 		r <- linkAnnex key (keyFilename source) (Just cache)
 		case r of
 			LinkAnnexFailed -> failure "failed to link to annex"
@@ -193,6 +196,34 @@ cleanCruft :: KeySource -> Annex ()
 cleanCruft source = when (contentLocation source /= keyFilename source) $
 	liftIO $ nukeFile $ contentLocation source
 
+-- If a worktree file was was hard linked to an annex object before,
+-- modifying the file would have caused the object to have the wrong
+-- content. Clean up from that.
+cleanOldKeys :: FilePath -> Key -> Annex ()
+cleanOldKeys file newkey = do
+	oldkeys <- filter (/= newkey)
+		<$> Database.Keys.getAssociatedKey file
+	mapM_ go oldkeys
+  where
+	go key = do
+		obj <- calcRepo (gitAnnexLocation key)
+		caches <- Database.Keys.getInodeCaches key
+		unlessM (sameInodeCache obj caches) $ do
+			unlinkAnnex key
+			fs <- filter (/= file)
+				<$> Database.Keys.getAssociatedFiles key
+			fs' <- filterM (`sameInodeCache` caches) fs
+			case fs' of
+				-- If linkAnnex fails, the associated 
+				-- file with the content is still present,
+				-- so no need for any recovery.
+				(f:_) -> do
+					ic <- withTSDelta (liftIO . genInodeCache f)
+					void $ linkAnnex key f ic
+				_ -> lostcontent
+	  where
+		lostcontent = logStatus key InfoMissing
+
 {- On error, put the file back so it doesn't seem to have vanished.
  - This can be called before or after the symlink is in place. -}
 restoreFile :: FilePath -> Key -> SomeException -> Annex a
diff --git a/Command/Smudge.hs b/Command/Smudge.hs
index 2876326b8b..5666381b05 100644
--- a/Command/Smudge.hs
+++ b/Command/Smudge.hs
@@ -74,39 +74,11 @@ clean file = do
 	if isJust (parseLinkOrPointer b)
 		then liftIO $ B.hPut stdout b
 		else ifM (shouldAnnex file)
-			( do
-				k <- ingest file
-				oldkeys <- filter (/= k)
-					<$> Database.Keys.getAssociatedKey file
-				mapM_ (cleanOldKey file) oldkeys
-				Database.Keys.addAssociatedFile k file
-				liftIO $ emitPointer k
+			( liftIO . emitPointer =<< ingest file
 			, liftIO $ B.hPut stdout b
 			)
 	stop
 
--- If the file being cleaned was hard linked to the old key's annex object,
--- modifying the file will have caused the object to have the wrong content.
--- Clean up from that.
-cleanOldKey :: FilePath -> Key -> Annex ()
-cleanOldKey modifiedfile key = do
-	obj <- calcRepo (gitAnnexLocation key)
-	caches <- Database.Keys.getInodeCaches key
-	unlessM (sameInodeCache obj caches) $ do
-		unlinkAnnex key
-		fs <- filter (/= modifiedfile)
-			<$> Database.Keys.getAssociatedFiles key
-		fs' <- filterM (`sameInodeCache` caches) fs
-		case fs' of
-			-- If linkAnnex fails, the file with the content
-			-- is still present, so no need for any recovery.
-			(f:_) -> do
-				ic <- withTSDelta (liftIO . genInodeCache f)
-				void $ linkAnnex key f ic
-			_ -> lostcontent
-  where
-	lostcontent = logStatus key InfoMissing
-
 shouldAnnex :: FilePath -> Annex Bool
 shouldAnnex file = do
 	matcher <- largeFilesMatcher