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.

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