completed the createDirectoryIfMissing conversion

Remaining calls in the assistant and Annex.Ssh have been audited and are ok.

Assistant/Threads/Merger.hs

@@ -26,8 +26,9 @@ import qualified Command.Sync
 mergeThread :: NamedThread
 mergeThread = namedThread "Merger" $ do
 	g <- liftAnnex gitRepo
-	let dir = fromRawFilePath (Git.localGitDir g) </> "refs"
-	liftIO $ createDirectoryIfMissing True dir
+	let gitd = fromRawFilePath (Git.localGitDir g)
+	let dir = gitd </> "refs"
+	liftIO $ createDirectoryUnder gitd dir
 	let hook a = Just <$> asIO2 (runHandler a)
 	changehook <- hook onChange
 	errhook <- hook onErr

Assistant/Threads/TransferWatcher.hs

@@ -15,6 +15,7 @@ import Logs.Transfer
 import Utility.DirWatcher
 import Utility.DirWatcher.Types
 import qualified Remote
+import Annex.Perms
 
 import Control.Concurrent
 import qualified Data.Map as M
@@ -24,7 +25,7 @@ import qualified Data.Map as M
 transferWatcherThread :: NamedThread
 transferWatcherThread = namedThread "TransferWatcher" $ do
 	dir <- liftAnnex $ gitAnnexTransferDir <$> gitRepo
-	liftIO $ createDirectoryIfMissing True dir
+	liftAnnex $ createAnnexDirectory dir
 	let hook a = Just <$> asIO2 (runHandler a)
 	addhook <- hook onAdd
 	delhook <- hook onDel

Assistant/WebApp/Configurators/Edit.hs

@@ -41,6 +41,7 @@ import Remote.Helper.Encryptable (extractCipher, parseEncryptionConfig)
 import Types.Crypto
 import Utility.Gpg
 import Annex.UUID
+import Annex.Perms
 import Assistant.Ssh
 import Config
 import Config.GitConfig
@@ -246,9 +247,9 @@ checkAssociatedDirectory cfg (Just r) = do
 	repoconfig <- M.lookup (Remote.uuid r) <$> readRemoteLog
 	case repoGroup cfg of
 		RepoGroupStandard gr -> case associatedDirectory repoconfig gr of
-			Just d -> inRepo $ \g ->
-				createDirectoryIfMissing True $
-					fromRawFilePath (Git.repoPath g) </> d
+			Just d -> do
+				top <- fromRawFilePath <$> fromRepo Git.repoPath
+				createWorkTreeDirectory (top </> d)
 			Nothing -> noop
 		_ -> noop