diff --git a/Assistant/Install.hs b/Assistant/Install.hs
index 94a40369cc..b2b7b91c62 100644
--- a/Assistant/Install.hs
+++ b/Assistant/Install.hs
@@ -17,6 +17,7 @@ import Utility.Shell
 import Utility.Tmp
 import Utility.Env
 import Utility.SshConfig
+import qualified Utility.FileIO as F
 
 #ifdef darwin_HOST_OS
 import Utility.OSX
@@ -126,17 +127,18 @@ installFileManagerHooks program = unlessM osAndroid $ do
 		(kdeDesktopFile actions)
   where
 	genNautilusScript scriptdir action =
-		installscript (scriptdir </> scriptname action) $ unlines
+		installscript (toRawFilePath (scriptdir </> scriptname action)) $ unlines
 			[ shebang
 			, autoaddedcomment
 			, "exec " ++ program ++ " " ++ action ++ " --notify-start --notify-finish -- \"$@\""
 			]
 	scriptname action = "git-annex " ++ action
 	installscript f c = whenM (safetoinstallscript f) $ do
-		writeFile f c
-		modifyFileMode (toRawFilePath f) $ addModes [ownerExecuteMode]
+		writeFile (fromRawFilePath f) c
+		modifyFileMode f $ addModes [ownerExecuteMode]
 	safetoinstallscript f = catchDefaultIO True $
-		elem autoaddedcomment . lines <$> readFileStrict f
+		elem (encodeBS autoaddedcomment) . fileLines'
+			<$> F.readFile' (toOsPath f)
 	autoaddedcomment = "# " ++ autoaddedmsg ++ " (To disable, chmod 600 this file.)"
 	autoaddedmsg = "Automatically added by git-annex, do not edit."
 
diff --git a/Assistant/Ssh.hs b/Assistant/Ssh.hs
index a85b294577..3a9235c76d 100644
--- a/Assistant/Ssh.hs
+++ b/Assistant/Ssh.hs
@@ -17,6 +17,7 @@ import Utility.SshConfig
 import Git.Remote
 import Utility.SshHost
 import Utility.Process.Transcript
+import qualified Utility.FileIO as F
 
 import Data.Text (Text)
 import qualified Data.Text as T
@@ -158,9 +159,9 @@ removeAuthorizedKeys :: Bool -> FilePath -> SshPubKey -> IO ()
 removeAuthorizedKeys gitannexshellonly dir pubkey = do
 	let keyline = authorizedKeysLine gitannexshellonly dir pubkey
 	sshdir <- sshDir
-	let keyfile = sshdir </> "authorized_keys"
-	tryWhenExists (lines <$> readFileStrict keyfile) >>= \case
-		Just ls -> viaTmp writeSshConfig (toOsPath (toRawFilePath keyfile)) $
+	let keyfile = toOsPath $ toRawFilePath $ sshdir </> "authorized_keys"
+	tryWhenExists (map decodeBS . fileLines' <$> F.readFile' keyfile) >>= \case
+		Just ls -> viaTmp writeSshConfig keyfile $
 			unlines $ filter (/= keyline) ls
 		Nothing -> noop
 
diff --git a/Config/Smudge.hs b/Config/Smudge.hs
index da198096fe..7d880c05cf 100644
--- a/Config/Smudge.hs
+++ b/Config/Smudge.hs
@@ -17,6 +17,7 @@ import Git.Types
 import Config
 import Utility.Directory.Create
 import Annex.Version
+import qualified Utility.FileIO as F
 
 import qualified System.FilePath.ByteString as P
 
@@ -65,9 +66,10 @@ stdattr =
 -- git-annex does not commit that.
 deconfigureSmudgeFilter :: Annex ()
 deconfigureSmudgeFilter = do
-	lf <- fromRawFilePath <$> Annex.fromRepo Git.attributesLocal
-	ls <- liftIO $ catchDefaultIO [] $ lines <$> readFileStrict lf
-	liftIO $ writeFile lf $ unlines $
+	lf <- Annex.fromRepo Git.attributesLocal
+	ls <- liftIO $ catchDefaultIO [] $ 
+		map decodeBS . fileLines' <$> F.readFile' (toOsPath lf)
+	liftIO $ writeFile (fromRawFilePath lf) $ unlines $
 		filter (\l -> l `notElem` stdattr && not (null l)) ls
 	unsetConfig (ConfigKey "filter.annex.smudge")
 	unsetConfig (ConfigKey "filter.annex.clean")
diff --git a/Logs/File.hs b/Logs/File.hs
index f385b06d66..93aef17f97 100644
--- a/Logs/File.hs
+++ b/Logs/File.hs
@@ -28,8 +28,6 @@ import Annex.ReplaceFile
 import Utility.Tmp
 import qualified Utility.FileIO as F
 
-import qualified Data.ByteString as S
-import qualified Data.ByteString.Char8 as S8
 import qualified Data.ByteString.Lazy as L
 import qualified Data.ByteString.Lazy.Char8 as L8
 
@@ -158,32 +156,3 @@ createDirWhenNeeded f a = a `catchNonAsync` \_e -> do
 	-- done if writing the file fails.
 	createAnnexDirectory (parentDir f)
 	a
-
--- On windows, readFile does NewlineMode translation,
--- stripping CR before LF. When converting to ByteString,
--- use this to emulate that.
-fileLines :: L.ByteString -> [L.ByteString]
-#ifdef mingw32_HOST_OS
-fileLines = map stripCR . L8.lines
-  where
-	stripCR b = case L8.unsnoc b of
-		Nothing -> b
-		Just (b', e)
-			| e == '\r' -> b'
-			| otherwise -> b
-#else
-fileLines = L8.lines
-#endif
-
-fileLines' :: S.ByteString -> [S.ByteString]
-#ifdef mingw32_HOST_OS
-fileLines' = map stripCR . S8.lines
-  where
-	stripCR b = case S8.unsnoc b of
-		Nothing -> b
-		Just (b', e)
-			| e == '\r' -> b'
-			| otherwise -> b
-#else
-fileLines' = S8.lines
-#endif
diff --git a/Upgrade/V7.hs b/Upgrade/V7.hs
index cad16f1854..0e301bd09d 100644
--- a/Upgrade/V7.hs
+++ b/Upgrade/V7.hs
@@ -22,6 +22,7 @@ import qualified Git
 import Git.FilePath
 import Config
 import qualified Utility.RawFilePath as R
+import qualified Utility.FileIO as F
 
 import qualified System.FilePath.ByteString as P
 import System.PosixCompat.Files (isSymbolicLink)
@@ -127,11 +128,12 @@ populateKeysDb = unlessM isBareRepo $ do
 -- checked into the repository.
 updateSmudgeFilter :: Annex ()
 updateSmudgeFilter = do
-	lf <- fromRawFilePath <$> Annex.fromRepo Git.attributesLocal
-	ls <- liftIO $ lines <$> catchDefaultIO "" (readFileStrict lf)
+	lf <- Annex.fromRepo Git.attributesLocal
+	ls <- liftIO $ map decodeBS . fileLines'
+		<$> catchDefaultIO "" (F.readFile' (toOsPath lf))
 	let ls' = removedotfilter ls
 	when (ls /= ls') $
-		liftIO $ writeFile lf (unlines ls')
+		liftIO $ writeFile (fromRawFilePath lf) (unlines ls')
   where
 	removedotfilter ("* filter=annex":".* !filter":rest) =
 		"* filter=annex" : removedotfilter rest
diff --git a/Utility/Misc.hs b/Utility/Misc.hs
index 7c00a184f4..d30cce2524 100644
--- a/Utility/Misc.hs
+++ b/Utility/Misc.hs
@@ -5,6 +5,7 @@
  - License: BSD-2-clause
  -}
 
+{-# LANGUAGE CPP #-}
 {-# OPTIONS_GHC -fno-warn-tabs #-}
 
 module Utility.Misc (
@@ -15,6 +16,8 @@ module Utility.Misc (
 	separateEnd',
 	firstLine,
 	firstLine',
+	fileLines,
+	fileLines',
 	segment,
 	segmentDelim,
 	massReplace,
@@ -32,6 +35,9 @@ import Data.List
 import System.Exit
 import Control.Applicative
 import qualified Data.ByteString as S
+import qualified Data.ByteString.Char8 as S8
+import qualified Data.ByteString.Lazy as L
+import qualified Data.ByteString.Lazy.Char8 as L8
 import Prelude
 
 {- A version of hgetContents that is not lazy. Ensures file is 
@@ -78,6 +84,35 @@ firstLine' = S.takeWhile (/= nl)
   where
 	nl = fromIntegral (ord '\n')
 
+-- On windows, readFile does NewlineMode translation,
+-- stripping CR before LF. When converting to ByteString,
+-- use this to emulate that.
+fileLines :: L.ByteString -> [L.ByteString]
+#ifdef mingw32_HOST_OS
+fileLines = map stripCR . L8.lines
+  where
+	stripCR b = case L8.unsnoc b of
+		Nothing -> b
+		Just (b', e)
+			| e == '\r' -> b'
+			| otherwise -> b
+#else
+fileLines = L8.lines
+#endif
+
+fileLines' :: S.ByteString -> [S.ByteString]
+#ifdef mingw32_HOST_OS
+fileLines' = map stripCR . S8.lines
+  where
+	stripCR b = case S8.unsnoc b of
+		Nothing -> b
+		Just (b', e)
+			| e == '\r' -> b'
+			| otherwise -> b
+#else
+fileLines' = S8.lines
+#endif
+
 {- Splits a list into segments that are delimited by items matching
  - a predicate. (The delimiters are not included in the segments.)
  - Segments may be empty. -}