diff --git a/Commands.hs b/Commands.hs
index da4d840ae1..6018ed8223 100644
--- a/Commands.hs
+++ b/Commands.hs
@@ -216,7 +216,7 @@ addCleanup file key = do
 	liftIO $ renameFile file dest
 	link <- calcGitLink file key
 	liftIO $ createSymbolicLink link file
-	liftIO $ Git.run g ["add", file]
+	Annex.queue "add" [] file
 	return True
 
 {- The unannex subcommand undoes an add. -}
@@ -340,11 +340,10 @@ fixPerform file link = do
 	liftIO $ createDirectoryIfMissing True (parentDir file)
 	liftIO $ removeFile file
 	liftIO $ createSymbolicLink link file
-	g <- Annex.gitRepo
-	liftIO $ Git.run g ["add", file]
-	return $ Just $ fixCleanup
-fixCleanup :: Annex Bool
-fixCleanup = do
+	return $ Just $ fixCleanup file
+fixCleanup :: FilePath -> Annex Bool
+fixCleanup file = do
+	Annex.queue "add" [] file
 	return True
 
 {- Stores description for the repository. -}
@@ -391,8 +390,7 @@ fromKeyPerform file key = do
 	return $ Just $ fromKeyCleanup file
 fromKeyCleanup :: FilePath -> Annex Bool
 fromKeyCleanup file = do
-	g <- Annex.gitRepo
-	liftIO $ Git.run g ["add", file]
+	Annex.queue "add" [] file
 	return True
 
 {- Move a file either --to or --from a repository.
@@ -453,7 +451,8 @@ moveToCleanup remote key tmpfile = do
 	-- Record that the key is present on the remote.
 	g <- Annex.gitRepo
 	remoteuuid <- getUUID remote
-	liftIO $ logChange g key remoteuuid ValuePresent
+	log <- liftIO $ logChange g key remoteuuid ValuePresent
+	Annex.queue "add" [] log
 	-- Cleanup on the local side is the same as done for the
 	-- drop subcommand.
 	dropCleanup key
@@ -492,7 +491,8 @@ moveFromCleanup remote key = do
 	-- Record locally that the key is not on the remote.
 	remoteuuid <- getUUID remote
 	g <- Annex.gitRepo
-	liftIO $ logChange g key remoteuuid ValueMissing
+	log <- liftIO $ logChange g key remoteuuid ValueMissing
+	Annex.queue "add" [] log
 	return True
 
 -- helpers
diff --git a/Core.hs b/Core.hs
index 4c7c9205e6..27baba28e6 100644
--- a/Core.hs
+++ b/Core.hs
@@ -39,8 +39,6 @@ shutdown = do
 			liftIO $ putStrLn "Recording state in git..."
 			liftIO $ GitQueue.run g q
 
-	liftIO $ Git.run g ["add", gitStateDir g]
-
 	-- clean up any files left in the temp directory, but leave
 	-- the tmp directory itself
 	let tmp = annexTmpLocation g
@@ -106,7 +104,8 @@ logStatus :: Key -> LogStatus -> Annex ()
 logStatus key status = do
 	g <- Annex.gitRepo
 	u <- getUUID g
-	liftIO $ logChange g key u status
+	log <- liftIO $ logChange g key u status
+	Annex.queue "add" [] log
 
 {- Runs an action, passing it a temporary filename to download,
  - and if the action succeeds, moves the temp file into 
diff --git a/LocationLog.hs b/LocationLog.hs
index 9ec71ce232..d027c4b809 100644
--- a/LocationLog.hs
+++ b/LocationLog.hs
@@ -82,12 +82,14 @@ instance Read LogLine where
 			undefined = ret $ LogLine (0) Undefined ""
 			ret v = [(v, "")]
 
-{- Log a change in the presence of a key's value in a repository. -}
-logChange :: Git.Repo -> Key -> UUID -> LogStatus -> IO ()
+{- Log a change in the presence of a key's value in a repository,
+ - and returns the filename of the logfile. -}
+logChange :: Git.Repo -> Key -> UUID -> LogStatus -> IO (FilePath)
 logChange repo key uuid status = do
 	log <- logNow status uuid
 	ls <- readLog logfile
 	writeLog logfile (compactLog $ log:ls)
+	return logfile
 	where
 		logfile = logFile repo key