diff --git a/Command/AddUrl.hs b/Command/AddUrl.hs
index 68ad7f0c34..de393fa669 100644
--- a/Command/AddUrl.hs
+++ b/Command/AddUrl.hs
@@ -20,6 +20,7 @@ import qualified Command.Add
 import Annex.Content
 import Annex.Ingest
 import Annex.CheckIgnore
+import Annex.Perms
 import Annex.UUID
 import Annex.YoutubeDl
 import Logs.Web
@@ -168,7 +169,7 @@ performRemote addunlockedmatcher r o uri file sz = ifAnnexed (toRawFilePath file
 downloadRemoteFile :: AddUnlockedMatcher -> Remote -> DownloadOptions -> URLString -> FilePath -> Maybe Integer -> Annex (Maybe Key)
 downloadRemoteFile addunlockedmatcher r o uri file sz = checkCanAdd file $ do
 	let urlkey = Backend.URL.fromUrl uri sz
-	liftIO $ createDirectoryIfMissing True (parentDir file)
+	createWorkTreeDirectory (parentDir file)
 	ifM (Annex.getState Annex.fast <||> pure (relaxedOption o))
 		( do
 			addWorkTree addunlockedmatcher (Remote.uuid r) loguri file urlkey Nothing
@@ -271,7 +272,7 @@ downloadWeb addunlockedmatcher o url urlinfo file =
 		)
 	normalfinish tmp = checkCanAdd file $ do
 		showDestinationFile file
-		liftIO $ createDirectoryIfMissing True (parentDir file)
+		createWorkTreeDirectory (parentDir file)
 		finishDownloadWith addunlockedmatcher tmp webUUID url file
 	tryyoutubedl tmp
 		-- Ask youtube-dl what filename it will download
@@ -357,7 +358,7 @@ downloadWith' downloader dummykey u url afile =
 		tmp <- fromRepo $ gitAnnexTmpObjectLocation dummykey
 		ok <- Transfer.notifyTransfer Transfer.Download url $
 			Transfer.download u dummykey afile Transfer.stdRetry $ \p -> do
-				liftIO $ createDirectoryIfMissing True (parentDir tmp)
+				createAnnexDirectory (parentDir tmp)
 				downloader tmp p
 		if ok
 			then return (Just tmp)
@@ -389,9 +390,9 @@ addWorkTree addunlockedmatcher u url file key mtmp = case mtmp of
 	Nothing -> go
 	Just tmp -> do
 		-- Move to final location for large file check.
-		pruneTmpWorkDirBefore tmp $ \_ -> liftIO $ do
-			createDirectoryIfMissing True (takeDirectory file)
-			renameFile tmp file
+		pruneTmpWorkDirBefore tmp $ \_ -> do
+			createWorkTreeDirectory (takeDirectory file)
+			liftIO $ renameFile tmp file
 		largematcher <- largeFilesMatcher
 		large <- checkFileMatcher largematcher file
 		if large
@@ -438,7 +439,7 @@ nodownloadWeb addunlockedmatcher o url urlinfo file
 nodownloadWeb' :: AddUnlockedMatcher -> URLString -> Key -> FilePath -> Annex (Maybe Key)
 nodownloadWeb' addunlockedmatcher url key file = checkCanAdd file $ do
 	showDestinationFile file
-	liftIO $ createDirectoryIfMissing True (parentDir file)
+	createWorkTreeDirectory (parentDir file)
 	addWorkTree addunlockedmatcher webUUID url file key Nothing
 	return (Just key)
 
diff --git a/Command/Fix.hs b/Command/Fix.hs
index 31ec91e586..5affc0590c 100644
--- a/Command/Fix.hs
+++ b/Command/Fix.hs
@@ -94,7 +94,7 @@ fixSymlink file link = do
 		mtime <- catchMaybeIO $ modificationTimeHiRes
 			<$> getSymbolicLinkStatus file
 #endif
-		createDirectoryIfMissing True (parentDir file)
+		createWorkTreeDirectory (parentDir file)
 		removeFile file
 		createSymbolicLink link file
 #if ! defined(mingw32_HOST_OS)
diff --git a/Command/FromKey.hs b/Command/FromKey.hs
index f3e7487272..5becd3b810 100644
--- a/Command/FromKey.hs
+++ b/Command/FromKey.hs
@@ -13,6 +13,7 @@ import Command
 import qualified Annex.Queue
 import Annex.Content
 import Annex.WorkTree
+import Annex.Perms
 import qualified Annex
 import qualified Backend.URL
 
@@ -85,7 +86,7 @@ perform key file = lookupFileNotHidden (toRawFilePath file) >>= \case
 		( hasothercontent
 		, do
 			link <- calcRepo $ gitAnnexLink file key
-			liftIO $ createDirectoryIfMissing True (parentDir file)
+			createWorkTreeDirectory (parentDir file)
 			liftIO $ createSymbolicLink link file
 			Annex.Queue.addCommand "add" [Param "--"] [file]
 			next $ return True
diff --git a/Command/Fsck.hs b/Command/Fsck.hs
index ead4c4f102..5d9d109856 100644
--- a/Command/Fsck.hs
+++ b/Command/Fsck.hs
@@ -219,7 +219,7 @@ fixLink key file = do
 	go want have
 		| want /= fromRawFilePath (fromInternalGitPath have) = do
 			showNote "fixing link"
-			liftIO $ createDirectoryIfMissing True (parentDir (fromRawFilePath file))
+			liftIO $ createWorkTreeDirectory (parentDir (fromRawFilePath file))
 			liftIO $ removeFile (fromRawFilePath file)
 			addAnnexLink want file
 		| otherwise = noop
diff --git a/Command/FuzzTest.hs b/Command/FuzzTest.hs
index 855d8c07d3..6bd1a0e1a8 100644
--- a/Command/FuzzTest.hs
+++ b/Command/FuzzTest.hs
@@ -13,6 +13,7 @@ import Command
 import qualified Annex
 import qualified Git.Config
 import Config
+import Annex.Perms
 import Utility.ThreadScheduler
 import Utility.DiskFree
 import Git.Types (fromConfigKey)
@@ -172,10 +173,10 @@ instance Arbitrary FuzzAction where
 		]
 
 runFuzzAction :: FuzzAction -> Annex ()
-runFuzzAction (FuzzAdd (FuzzFile f)) = liftIO $ do
-	createDirectoryIfMissing True $ parentDir f
-	n <- getStdRandom random :: IO Int
-	writeFile f $ show n ++ "\n"
+runFuzzAction (FuzzAdd (FuzzFile f)) = do
+	createWorkTreeDirectory (parentDir f)
+	n <- liftIO (getStdRandom random :: IO Int)
+	liftIO $ writeFile f $ show n ++ "\n"
 runFuzzAction (FuzzDelete (FuzzFile f)) = liftIO $ nukeFile f
 runFuzzAction (FuzzMove (FuzzFile src) (FuzzFile dest)) = liftIO $
 	rename src dest
diff --git a/Command/Import.hs b/Command/Import.hs
index 69b535644a..5447df5bff 100644
--- a/Command/Import.hs
+++ b/Command/Import.hs
@@ -25,6 +25,7 @@ import Annex.FileMatcher
 import Annex.Ingest
 import Annex.InodeSentinal
 import Annex.Import
+import Annex.Perms
 import Annex.RemoteTrackingBranch
 import Utility.InodeCache
 import Logs.Location
@@ -176,12 +177,12 @@ startLocal addunlockedmatcher largematcher mode (srcfile, destfile) =
 	importfilechecked ld k = do
 		-- Move or copy the src file to the dest file.
 		-- The dest file is what will be ingested.
-		liftIO $ createDirectoryIfMissing True (parentDir destfile)
+		createWorkTreeDirectory (parentDir destfile)
 		liftIO $ if mode == Duplicate || mode == SkipDuplicates
 			then void $ copyFileExternal CopyAllMetaData srcfile destfile
 			else moveFile srcfile destfile
 		-- Get the inode cache of the dest file. It should be
-		-- weakly the same as the origianlly locked down file's
+		-- weakly the same as the originally locked down file's
 		-- inode cache. (Since the file may have been copied,
 		-- its inodes may not be the same.)
 		newcache <- withTSDelta $ liftIO . genInodeCache destfile'
diff --git a/Database/Init.hs b/Database/Init.hs
index 3744de6582..c66fe43acf 100644
--- a/Database/Init.hs
+++ b/Database/Init.hs
@@ -10,7 +10,6 @@ module Database.Init where
 import Annex.Common
 import Annex.Perms
 import Utility.FileMode
-import Utility.Directory
 
 import Database.Persist.Sqlite
 import Control.Monad.IO.Class (liftIO)
diff --git a/Git/Repair.hs b/Git/Repair.hs
index 66e68117f3..10ea6a8ddc 100644
--- a/Git/Repair.hs
+++ b/Git/Repair.hs
@@ -245,8 +245,9 @@ explodePackedRefsFile r = do
 		nukeFile f
   where
 	makeref (sha, ref) = do
-		let dest = fromRawFilePath (localGitDir r) </> fromRef ref
-		createDirectoryIfMissing True (parentDir dest)
+		let gitd = fromRawFilePath (localGitDir r)
+		let dest = gitd </> fromRef ref
+		createDirectoryUnder gitd (parentDir dest)
 		unlessM (doesFileExist dest) $
 			writeFile dest (fromRef sha)
 
diff --git a/Remote/GCrypt.hs b/Remote/GCrypt.hs
index a50d949d26..6416a18d5b 100644
--- a/Remote/GCrypt.hs
+++ b/Remote/GCrypt.hs
@@ -49,6 +49,7 @@ import qualified Remote.Helper.Ssh as Ssh
 import Utility.Metered
 import Annex.UUID
 import Annex.Ssh
+import Annex.Perms
 import qualified Remote.Rsync
 import qualified Remote.Directory
 import Utility.Rsync
@@ -283,7 +284,7 @@ setupRepo gcryptid r
 	 - which is needed for direct rsync of objects to work.
 	 -}
 	rsyncsetup = Remote.Rsync.withRsyncScratchDir $ \tmp -> do
-		liftIO $ createDirectoryIfMissing True $ tmp </> objectDir
+		createAnnexDirectory (tmp </> objectDir)
 		dummycfg <- liftIO dummyRemoteGitConfig
 		(rsynctransport, rsyncurl, _) <- rsyncTransport r dummycfg
 		let tmpconfig = tmp </> "config"
@@ -368,7 +369,7 @@ store' repo r rsyncopts
 	| not $ Git.repoIsUrl repo = 
 		byteStorer $ \k b p -> guardUsable repo (return False) $ liftIO $ do
 			let tmpdir = Git.repoLocation repo </> "tmp" </> fromRawFilePath (keyFile k)
-			void $ tryIO $ createDirectoryIfMissing True tmpdir
+			void $ tryIO $ createDirectoryUnder (Git.repoLocation repo) tmpdir
 			let tmpf = tmpdir </> fromRawFilePath (keyFile k)
 			meteredWriteFile p tmpf b
 			let destdir = parentDir $ gCryptLocation repo k
diff --git a/Remote/Rsync.hs b/Remote/Rsync.hs
index b19bbbe78b..04d01e60a3 100644
--- a/Remote/Rsync.hs
+++ b/Remote/Rsync.hs
@@ -27,6 +27,7 @@ import Config.Cost
 import Annex.Content
 import Annex.UUID
 import Annex.Ssh
+import Annex.Perms
 import Remote.Helper.Special
 import Remote.Helper.Messages
 import Remote.Helper.ExportImport
@@ -218,7 +219,7 @@ store o k src meterupdate = storeGeneric o meterupdate basedest populatedest
 storeGeneric :: RsyncOpts -> MeterUpdate -> FilePath -> (FilePath -> Annex Bool) -> Annex Bool
 storeGeneric o meterupdate basedest populatedest = withRsyncScratchDir $ \tmp -> do
 	let dest = tmp </> basedest
-	liftIO $ createDirectoryIfMissing True $ parentDir dest
+	createAnnexDirectory (parentDir dest)
 	ok <- populatedest dest
 	ps <- sendParams
 	if ok
diff --git a/Upgrade/V1.hs b/Upgrade/V1.hs
index 88a3494484..ddf54aa123 100644
--- a/Upgrade/V1.hs
+++ b/Upgrade/V1.hs
@@ -17,6 +17,7 @@ import qualified Data.ByteString.Lazy as L
 import Annex.Common
 import Annex.Content
 import Annex.Link
+import Annex.Perms
 import Types.Key
 import Logs.Presence
 import qualified Annex.Queue
@@ -115,7 +116,7 @@ moveLocationLogs = do
 		dest <- fromRepo $ logFile2 k
 		dir <- fromRepo Upgrade.V2.gitStateDir
 		let f = dir </> l
-		liftIO $ createDirectoryIfMissing True (parentDir dest)
+		createWorkTreeDirectory (parentDir dest)
 		-- could just git mv, but this way deals with
 		-- log files that are not checked into git,
 		-- as well as merging with already upgraded