avoid confusing git with a modified ctime in clean filter

Linking the file to the tmp dir was not necessary in the clean
filter, and it caused the ctime to change, which caused git to think
the file was changed. This caused git status to get slow as it kept
re-cleaning unchanged files.

Annex/Ingest.hs

@@ -9,6 +9,7 @@
 
 module Annex.Ingest (
 	LockedDown(..),
+	LockDownConfig(..),
 	lockDown,
 	ingest,
 	finishIngestDirect,
@@ -48,11 +49,17 @@ import Utility.Touch
 import Control.Exception (IOException)
 
 data LockedDown = LockedDown
-	{ lockingFile :: Bool
+	{ lockDownConfig :: LockDownConfig
 	, keySource :: KeySource
 	}
 	deriving (Show)
 
+data LockDownConfig = LockDownConfig
+	{ lockingFile :: Bool -- ^ write bit removed during lock down
+	, hardlinkFileTmp :: Bool -- ^ hard link to temp directory
+	}
+	deriving (Show)
+
 {- The file that's being ingested is locked down before a key is generated,
  - to prevent it from being modified in between. This lock down is not
  - perfect at best (and pretty weak at worst). For example, it does not
@@ -64,24 +71,21 @@ data LockedDown = LockedDown
  - against some changes, like deletion or overwrite of the file, and
  - allows lsof checks to be done more efficiently when adding a lot of files.
  -
- - If lockingfile is True, the file is going to be added in locked mode.
- - So, its write bit is removed as part of the lock down.
- -
  - Lockdown can fail if a file gets deleted, and Nothing will be returned.
  -}
-lockDown :: Bool -> FilePath -> Annex (Maybe LockedDown)
-lockDown lockingfile file = either 
+lockDown :: LockDownConfig -> FilePath -> Annex (Maybe LockedDown)
+lockDown cfg file = either 
 		(\e -> warning (show e) >> return Nothing)
 		(return . Just)
-	=<< lockDown' lockingfile file
+	=<< lockDown' cfg file
 
-lockDown' :: Bool -> FilePath -> Annex (Either IOException LockedDown)
-lockDown' lockingfile file = ifM crippledFileSystem
+lockDown' :: LockDownConfig -> FilePath -> Annex (Either IOException LockedDown)
+lockDown' cfg file = ifM (pure (not (hardlinkFileTmp cfg)) <||> crippledFileSystem)
 	( withTSDelta $ liftIO . tryIO . nohardlink
 	, tryIO $ do
 		tmp <- fromRepo gitAnnexTmpMiscDir
 		createAnnexDirectory tmp
-		when lockingfile $
+		when (lockingFile cfg) $
 			freezeContent file
 		withTSDelta $ \delta -> liftIO $ do
 			(tmpfile, h) <- openTempFile tmp $
@@ -93,7 +97,7 @@ lockDown' lockingfile file = ifM crippledFileSystem
   where
 	nohardlink delta = do
 		cache <- genInodeCache file delta
-		return $ LockedDown lockingfile $ KeySource
+		return $ LockedDown cfg $ KeySource
 			{ keyFilename = file
 			, contentLocation = file
 			, inodeCache = cache
@@ -101,7 +105,7 @@ lockDown' lockingfile file = ifM crippledFileSystem
 	withhardlink delta tmpfile = do
 		createLink file tmpfile
 		cache <- genInodeCache tmpfile delta
-		return $ LockedDown lockingfile $ KeySource
+		return $ LockedDown cfg $ KeySource
 			{ keyFilename = file
 			, contentLocation = tmpfile
 			, inodeCache = cache
@@ -115,7 +119,7 @@ lockDown' lockingfile file = ifM crippledFileSystem
  -}
 ingest :: Maybe LockedDown -> Annex (Maybe Key, Maybe InodeCache)
 ingest Nothing = return (Nothing, Nothing)
-ingest (Just (LockedDown lockingfile source)) = withTSDelta $ \delta -> do
+ingest (Just (LockedDown cfg source)) = withTSDelta $ \delta -> do
 	backend <- chooseBackend $ keyFilename source
 	k <- genKey source backend
 	let src = contentLocation source
@@ -127,7 +131,7 @@ ingest (Just (LockedDown lockingfile source)) = withTSDelta $ \delta -> do
 		_ -> failure "changed while it was being added"
   where
 	go (Just (key, _)) mcache (Just s)
-		| lockingfile = golocked key mcache s
+		| lockingFile cfg = golocked key mcache s
 		| otherwise = ifM isDirect
 			( godirect key mcache s
 			, gounlocked key mcache s

Assistant/Threads/Committer.hs

@@ -268,11 +268,15 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 	direct <- liftAnnex isDirect
 	unlocked <- liftAnnex versionSupportsUnlockedPointers
 	let lockingfiles = not (unlocked || direct)
+	let lockdownconfig = LockDownConfig
+		{ lockingFile = lockingfiles
+		, hardlinkFileTmp = True
+		}
 	(pending', cleanup) <- if unlocked || direct
 		then return (pending, noop)
 		else findnew pending
 	(postponed, toadd) <- partitionEithers
-		<$> safeToAdd lockingfiles havelsof delayadd pending' inprocess
+		<$> safeToAdd lockdownconfig havelsof delayadd pending' inprocess
 	cleanup
 
 	unless (null postponed) $
@@ -283,7 +287,7 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 			catMaybes <$>
 				if not lockingfiles
 					then addunlocked direct toadd
-					else forM toadd (add lockingfiles)
+					else forM toadd (add lockdownconfig)
 		if DirWatcher.eventsCoalesce || null added || unlocked || direct
 			then return $ added ++ otherchanges
 			else do
@@ -310,15 +314,15 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 		| c = return otherchanges
 		| otherwise = a
 
-	add :: Bool -> Change -> Assistant (Maybe Change)
-	add lockingfile change@(InProcessAddChange { lockedDown = ld }) = 
+	add :: LockDownConfig -> Change -> Assistant (Maybe Change)
+	add lockdownconfig change@(InProcessAddChange { lockedDown = ld }) = 
 		catchDefaultIO Nothing <~> doadd
 	  where
 	  	ks = keySource ld
 		doadd = sanitycheck ks $ do
 			(mkey, mcache) <- liftAnnex $ do
 				showStart "add" $ keyFilename ks
-				ingest $ Just $ LockedDown lockingfile ks
+				ingest $ Just $ LockedDown lockdownconfig ks
 			maybe (failedingest change) (done change mcache $ keyFilename ks) mkey
 	add _ _ = return Nothing
 
@@ -332,15 +336,19 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
 		ct <- liftAnnex compareInodeCachesWith
 		m <- liftAnnex $ removedKeysMap isdirect ct cs
 		delta <- liftAnnex getTSDelta
+		let cfg = LockDownConfig
+			{ lockingFile = False
+			, hardlinkFileTmp = True
+			}
 		if M.null m
-			then forM toadd (add False)
+			then forM toadd (add cfg)
 			else forM toadd $ \c -> do
 				mcache <- liftIO $ genInodeCache (changeFile c) delta
 				case mcache of
-					Nothing -> add False c
+					Nothing -> add cfg c
 					Just cache ->
 						case M.lookup (inodeCacheToKey ct cache) m of
-							Nothing -> add False c
+							Nothing -> add cfg c
 							Just k -> fastadd isdirect c k
 
 	fastadd :: Bool -> Change -> Key -> Assistant (Maybe Change)
@@ -416,12 +424,12 @@ handleAdds havelsof delayadd cs = returnWhen (null incomplete) $ do
  -
  - Check by running lsof on the repository.
  -}
-safeToAdd :: Bool -> Bool -> Maybe Seconds -> [Change] -> [Change] -> Assistant [Either Change Change]
+safeToAdd :: LockDownConfig -> Bool -> Maybe Seconds -> [Change] -> [Change] -> Assistant [Either Change Change]
 safeToAdd _ _ _ [] [] = return []
-safeToAdd lockingfiles havelsof delayadd pending inprocess = do
+safeToAdd lockdownconfig havelsof delayadd pending inprocess = do
 	maybe noop (liftIO . threadDelaySeconds) delayadd
 	liftAnnex $ do
-		lockeddown <- forM pending $ lockDown lockingfiles . changeFile
+		lockeddown <- forM pending $ lockDown lockdownconfig . changeFile
 		let inprocess' = inprocess ++ mapMaybe mkinprocess (zip pending lockeddown)
 		openfiles <- if havelsof
 			then S.fromList . map fst3 . filter openwrite <$>

Command/Add.hs

@@ -115,7 +115,11 @@ start file = ifAnnexed file addpresent add
 perform :: FilePath -> CommandPerform
 perform file = do
 	lockingfile <- not <$> isDirect
-	lockDown lockingfile file >>= ingest >>= go
+	let cfg = LockDownConfig
+		{ lockingFile = lockingfile
+		, hardlinkFileTmp = True
+		}
+	lockDown cfg file >>= ingest >>= go
   where
 	go (Just key, cache) = next $ cleanup file key cache True
 	go (Nothing, _) = stop

Command/Smudge.hs

@@ -72,7 +72,7 @@ clean file = do
 		then liftIO $ B.hPut stdout b
 		else ifM (shouldAnnex file)
 			( liftIO . emitPointer
-				=<< go =<< ingest =<< lockDown False file
+				=<< go =<< ingest =<< lockDown cfg file
 			, liftIO $ B.hPut stdout b
 			)
 	stop
@@ -81,6 +81,10 @@ clean file = do
 		logStatus k InfoPresent
 		return k
 	go _ = error "could not add file to the annex"
+	cfg = LockDownConfig
+		{ lockingFile = False
+		, hardlinkFileTmp = False
+		}
 
 shouldAnnex :: FilePath -> Annex Bool
 shouldAnnex file = do