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.

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