diff --git a/Annex/Direct.hs b/Annex/Direct.hs
index 8fced2d444..8c3d5bb562 100644
--- a/Annex/Direct.hs
+++ b/Annex/Direct.hs
@@ -399,7 +399,7 @@ changedDirect oldk f = do
 	whenM (pure (null locs) <&&> not <$> inAnnex oldk) $
 		logStatus oldk InfoMissing
 
-{- Enable/disable direct mode. -}
+{- Git config settings to enable/disable direct mode. -}
 setDirect :: Bool -> Annex ()
 setDirect wantdirect = do
 	if wantdirect
diff --git a/Annex/View.hs b/Annex/View.hs
index 567522a541..8ddbb9c638 100644
--- a/Annex/View.hs
+++ b/Annex/View.hs
@@ -22,7 +22,7 @@ import Git.Sha
 import Git.HashObject
 import Git.Types
 import Git.FilePath
-import qualified Backend
+import Annex.WorkTree
 import Annex.Index
 import Annex.Link
 import Annex.CatFile
@@ -342,7 +342,7 @@ applyView' mkviewedfile getfilemetadata view = do
 		hasher <- inRepo hashObjectStart
 		forM_ l $ \f -> do
 			relf <- getTopFilePath <$> inRepo (toTopFilePath f)
-			go uh hasher relf =<< Backend.lookupFile f
+			go uh hasher relf =<< lookupFile f
 		liftIO $ do
 			hashObjectStop hasher
 			void $ stopUpdateIndex uh
diff --git a/Annex/WorkTree.hs b/Annex/WorkTree.hs
new file mode 100644
index 0000000000..26144e7f9e
--- /dev/null
+++ b/Annex/WorkTree.hs
@@ -0,0 +1,35 @@
+{- git-annex worktree files
+ -
+ - Copyright 2013-2015 Joey Hess <id@joeyh.name>
+ -
+ - Licensed under the GNU GPL version 3 or higher.
+ -}
+
+module Annex.WorkTree where
+
+import Common.Annex
+import Annex.Link
+import Annex.CatFile
+
+{- Looks up the key corresponding to an annexed file,
+ - by examining what the file links to.
+ -
+ - An unlocked file will not have a link on disk, so fall back to
+ - looking for a pointer to a key in git.
+ -}
+lookupFile :: FilePath -> Annex (Maybe Key)
+lookupFile file = do
+	mkey <- isAnnexLink file
+	case mkey of
+		Just key -> makeret key
+		Nothing -> maybe (return Nothing) makeret =<< catKeyFile file
+  where
+	makeret = return . Just
+
+{- Modifies an action to only act on files that are already annexed,
+ - and passes the key on to it. -}
+whenAnnexed :: (FilePath -> Key -> Annex (Maybe a)) -> FilePath -> Annex (Maybe a)
+whenAnnexed a file = ifAnnexed file (a file) (return Nothing)
+
+ifAnnexed :: FilePath -> (Key -> Annex a) -> Annex a -> Annex a
+ifAnnexed file yes no = maybe no yes =<< lookupFile file
diff --git a/Assistant/Threads/TransferScanner.hs b/Assistant/Threads/TransferScanner.hs
index f35c1f1f53..7386d55286 100644
--- a/Assistant/Threads/TransferScanner.hs
+++ b/Assistant/Threads/TransferScanner.hs
@@ -25,7 +25,7 @@ import Utility.ThreadScheduler
 import Utility.NotificationBroadcaster
 import Utility.Batch
 import qualified Git.LsFiles as LsFiles
-import qualified Backend
+import Annex.WorkTree
 import Annex.Content
 import Annex.Wanted
 import CmdLine.Action
@@ -142,7 +142,7 @@ expensiveScan urlrenderer rs = batch <~> do
 		(unwanted', ts) <- maybe
 			(return (unwanted, []))
 			(findtransfers f unwanted)
-				=<< liftAnnex (Backend.lookupFile f)
+				=<< liftAnnex (lookupFile f)
 		mapM_ (enqueue f) ts
 		scan unwanted' fs
 
diff --git a/Assistant/Threads/Watcher.hs b/Assistant/Threads/Watcher.hs
index 8c6ff378dd..37e0154b45 100644
--- a/Assistant/Threads/Watcher.hs
+++ b/Assistant/Threads/Watcher.hs
@@ -28,7 +28,7 @@ import qualified Annex.Queue
 import qualified Git
 import qualified Git.UpdateIndex
 import qualified Git.LsFiles as LsFiles
-import qualified Backend
+import Annex.WorkTree
 import Annex.Direct
 import Annex.Content.Direct
 import Annex.CatFile
@@ -270,7 +270,7 @@ onAddDirect symlinkssupported matcher file fs = do
 onAddSymlink :: Bool -> Handler
 onAddSymlink isdirect file filestatus = unlessIgnored file $ do
 	linktarget <- liftIO (catchMaybeIO $ readSymbolicLink file)
-	kv <- liftAnnex (Backend.lookupFile file)
+	kv <- liftAnnex (lookupFile file)
 	onAddSymlink' linktarget kv isdirect file filestatus
 
 onAddSymlink' :: Maybe String -> Maybe Key -> Bool -> Handler
diff --git a/Backend.hs b/Backend.hs
index d37eed34af..c2f3d28d41 100644
--- a/Backend.hs
+++ b/Backend.hs
@@ -9,7 +9,6 @@ module Backend (
 	list,
 	orderedList,
 	genKey,
-	lookupFile,
 	getBackend,
 	chooseBackend,
 	lookupBackendName,
@@ -20,8 +19,6 @@ module Backend (
 import Common.Annex
 import qualified Annex
 import Annex.CheckAttr
-import Annex.CatFile
-import Annex.Link
 import Types.Key
 import Types.KeySource
 import qualified Types.Backend as B
@@ -76,21 +73,6 @@ genKey' (b:bs) source = do
 		| c == '\n' = '_'
 		| otherwise = c
 
-{- Looks up the key corresponding to an annexed file,
- - by examining what the file links to.
- -
- - An unlocked file will not have a link on disk, so fall back to
- - looking for a pointer to a key in git.
- -}
-lookupFile :: FilePath -> Annex (Maybe Key)
-lookupFile file = do
-	mkey <- isAnnexLink file
-	case mkey of
-		Just key -> makeret key
-		Nothing -> maybe (return Nothing) makeret =<< catKeyFile file
-  where
-	makeret = return . Just
-
 getBackend :: FilePath -> Key -> Annex (Maybe Backend)
 getBackend file k = let bname = keyBackendName k in
 	case maybeLookupBackendName bname of
diff --git a/Command.hs b/Command.hs
index bee63bb741..387f7b8b56 100644
--- a/Command.hs
+++ b/Command.hs
@@ -18,12 +18,13 @@ module Command (
 	stopUnless,
 	whenAnnexed,
 	ifAnnexed,
+	lookupFile,
 	isBareRepo,
 	module ReExported
 ) where
 
 import Common.Annex
-import qualified Backend
+import Annex.WorkTree
 import qualified Git
 import Types.Command as ReExported
 import Types.Option as ReExported
@@ -100,13 +101,5 @@ stop = return Nothing
 stopUnless :: Annex Bool -> Annex (Maybe a) -> Annex (Maybe a)
 stopUnless c a = ifM c ( a , stop )
 
-{- Modifies an action to only act on files that are already annexed,
- - and passes the key on to it. -}
-whenAnnexed :: (FilePath -> Key -> Annex (Maybe a)) -> FilePath -> Annex (Maybe a)
-whenAnnexed a file = ifAnnexed file (a file) (return Nothing)
-
-ifAnnexed :: FilePath -> (Key -> Annex a) -> Annex a -> Annex a
-ifAnnexed file yes no = maybe no yes =<< Backend.lookupFile file
-
 isBareRepo :: Annex Bool
 isBareRepo = fromRepo Git.repoIsLocalBare
diff --git a/Command/Unused.hs b/Command/Unused.hs
index 4756cda5df..4353bd075e 100644
--- a/Command/Unused.hs
+++ b/Command/Unused.hs
@@ -24,7 +24,6 @@ import qualified Git.Branch
 import qualified Git.RefLog
 import qualified Git.LsFiles as LsFiles
 import qualified Git.DiffTree as DiffTree
-import qualified Backend
 import qualified Remote
 import qualified Annex.Branch
 import Annex.CatFile
@@ -215,7 +214,7 @@ withKeysReferenced' mdir initial a = do
 		Just dir -> inRepo $ LsFiles.inRepo [dir]
 	go v [] = return v
 	go v (f:fs) = do
-		x <- Backend.lookupFile f
+		x <- lookupFile f
 		case x of
 			Nothing -> go v fs
 			Just k -> do
@@ -266,7 +265,7 @@ withKeysReferencedInGitRef a ref = do
 	forM_ ts $ tKey lookAtWorkingTree >=> maybe noop a
 	liftIO $ void clean
   where
-	tKey True = Backend.lookupFile . getTopFilePath . DiffTree.file
+	tKey True = lookupFile . getTopFilePath . DiffTree.file
 	tKey False = fileKey . takeFileName . decodeBS <$$>
 		catFile ref . getTopFilePath . DiffTree.file
 
diff --git a/Command/Upgrade.hs b/Command/Upgrade.hs
index c02a6709f9..8a34022e3c 100644
--- a/Command/Upgrade.hs
+++ b/Command/Upgrade.hs
@@ -13,6 +13,7 @@ import Upgrade
 
 cmd :: Command
 cmd = dontCheck repoExists $ -- because an old version may not seem to exist
+	noDaemonRunning $ -- avoid upgrading repo out from under daemon
 	command "upgrade" SectionMaintenance "upgrade repository layout"
 		paramNothing (withParams seek)
 
diff --git a/Limit.hs b/Limit.hs
index 321c1122b3..437c65bc35 100644
--- a/Limit.hs
+++ b/Limit.hs
@@ -11,8 +11,8 @@ import Common.Annex
 import qualified Annex
 import qualified Utility.Matcher
 import qualified Remote
-import qualified Backend
 import Annex.Content
+import Annex.WorkTree
 import Annex.Action
 import Annex.UUID
 import Logs.Trust
@@ -277,7 +277,7 @@ addTimeLimit s = do
 			else return True
 
 lookupFileKey :: FileInfo -> Annex (Maybe Key)
-lookupFileKey = Backend.lookupFile . currFile
+lookupFileKey = lookupFile . currFile
 
 checkKey :: (Key -> Annex Bool) -> MatchInfo -> Annex Bool
 checkKey a (MatchingFile fi) = lookupFileKey fi >>= maybe (return False) a
diff --git a/Test.hs b/Test.hs
index f4035f6051..1a0601b35c 100644
--- a/Test.hs
+++ b/Test.hs
@@ -65,6 +65,7 @@ import qualified Types.Messages
 import qualified Config
 import qualified Config.Cost
 import qualified Crypto
+import qualified Annex.WorkTree
 import qualified Annex.Init
 import qualified Annex.CatFile
 import qualified Annex.View
@@ -810,7 +811,7 @@ test_unused = intmpclonerepoInDirect $ do
 		assertEqual ("unused keys differ " ++ desc)
 			(sort expectedkeys) (sort unusedkeys)
 	findkey f = do
-		r <- Backend.lookupFile f
+		r <- Annex.WorkTree.lookupFile f
 		return $ fromJust r
 
 test_describe :: Assertion
@@ -1380,7 +1381,7 @@ test_crypto = do
 			(c,k) <- annexeval $ do
 				uuid <- Remote.nameToUUID "foo"
 				rs <- Logs.Remote.readRemoteLog
-				Just k <- Backend.lookupFile annexedfile
+				Just k <- Annex.WorkTree.lookupFile annexedfile
 				return (fromJust $ M.lookup uuid rs, k)
 			let key = if scheme `elem` ["hybrid","pubkey"]
 					then Just $ Utility.Gpg.KeyIds [Utility.Gpg.testKeyId]
@@ -1684,7 +1685,7 @@ checkdangling f = ifM (annexeval Config.crippledFileSystem)
 checklocationlog :: FilePath -> Bool -> Assertion
 checklocationlog f expected = do
 	thisuuid <- annexeval Annex.UUID.getUUID
-	r <- annexeval $ Backend.lookupFile f
+	r <- annexeval $ Annex.WorkTree.lookupFile f
 	case r of
 		Just k -> do
 			uuids <- annexeval $ Remote.keyLocations k
@@ -1695,7 +1696,7 @@ checklocationlog f expected = do
 checkbackend :: FilePath -> Types.Backend -> Assertion
 checkbackend file expected = do
 	b <- annexeval $ maybe (return Nothing) (Backend.getBackend file) 
-		=<< Backend.lookupFile file
+		=<< Annex.WorkTree.lookupFile file
 	assertEqual ("backend for " ++ file) (Just expected) b
 
 inlocationlog :: FilePath -> Assertion