mostly finished with createDirectoryUnder conversion

Remaining things needing converted are in the assistant, and Annex.Ssh.

Every other remaining call to createDirectoryIfMissing True has been
audited and is not relevant. The ones in Build/ of course don't get
included in the program. Others included eg, Remote.Tahoe and
Config.Files which both write to dotfiles under the home directory.

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