remove some unncessary uses of warningIO

warningIO is not concurrent output safe, and it doesn't go to
--json-error-messages

There are a few more that would be too hard to remove, and there are also
several dozen direct prints to stderr still.

Assistant/Threads/Watcher.hs

@@ -183,7 +183,7 @@ runHandler :: Handler -> FilePath -> Maybe FileStatus -> Assistant ()
 runHandler handler file filestatus = void $ do
 	r <- tryIO <~> handler (normalize file) filestatus
 	case r of
-		Left e -> liftIO $ warningIO $ show e
+		Left e -> liftAnnex $ warning $ show e
 		Right Nothing -> noop
 		Right (Just change) -> recordChange change
   where

Remote/GCrypt.hs

@@ -286,7 +286,7 @@ setupRepo gcryptid r
 	{-  Ask git-annex-shell to configure the repository as a gcrypt
 	 -  repository. May fail if it is too old. -}
 	gitannexshellsetup = Ssh.onRemote NoConsumeStdin r
-		(boolSystem, return False)
+		(\f p -> liftIO (boolSystem f p), return False)
 		"gcryptsetup" [ Param gcryptid ] []
 
 	denyNonFastForwards = "receive.denyNonFastForwards"
@@ -451,7 +451,7 @@ getGCryptId fast r gc
 	| Git.repoIsLocal r || Git.repoIsLocalUnknown r = extract <$>
 		liftIO (catchMaybeIO $ Git.Config.read r)
 	| not fast = extract . liftM fst <$> getM (eitherToMaybe <$>)
-		[ Ssh.onRemote NoConsumeStdin r (Git.Config.fromPipe r, return (Left $ error "configlist failed")) "configlist" [] []
+		[ Ssh.onRemote NoConsumeStdin r (\f p -> liftIO (Git.Config.fromPipe r f p), return (Left $ error "configlist failed")) "configlist" [] []
 		, getConfigViaRsync r gc
 		]
 	| otherwise = return (Nothing, r)

Remote/Git.hs

@@ -249,21 +249,21 @@ tryGitConfigRead autoinit r
 	haveconfig = not . M.null . Git.config
 
 	pipedconfig cmd params = do
-		v <- Git.Config.fromPipe r cmd params
+		v <- liftIO $ Git.Config.fromPipe r cmd params
 		case v of
 			Right (r', val) -> do
 				unless (isUUIDConfigured r' || null val) $ do
-					warningIO $ "Failed to get annex.uuid configuration of repository " ++ Git.repoDescribe r
-					warningIO $ "Instead, got: " ++ show val
-					warningIO $ "This is unexpected; please check the network transport!"
+					warning $ "Failed to get annex.uuid configuration of repository " ++ Git.repoDescribe r
+					warning $ "Instead, got: " ++ show val
+					warning $ "This is unexpected; please check the network transport!"
 				return $ Right r'
 			Left l -> return $ Left l
 
 	geturlconfig = Url.withUrlOptions $ \uo -> do
-		v <- liftIO $ withTmpFile "git-annex.tmp" $ \tmpfile h -> do
-			hClose h
+		v <- withTmpFile "git-annex.tmp" $ \tmpfile h -> do
+			liftIO $ hClose h
 			let url = Git.repoLocation r ++ "/config"
-			ifM (Url.downloadQuiet nullMeterUpdate url tmpfile uo)
+			ifM (liftIO $ Url.downloadQuiet nullMeterUpdate url tmpfile uo)
 				( Just <$> pipedconfig "git" [Param "config", Param "--null", Param "--list", Param "--file", File tmpfile]
 				, return Nothing
 				)

Remote/Helper/Ssh.hs

@@ -83,7 +83,7 @@ git_annex_shell cs r command params fields
 onRemote 
 	:: ConsumeStdin
 	-> Git.Repo
-	-> (FilePath -> [CommandParam] -> IO a, Annex a)
+	-> (FilePath -> [CommandParam] -> Annex a, Annex a)
 	-> String
 	-> [CommandParam]
 	-> [(Field, String)]
@@ -91,7 +91,7 @@ onRemote
 onRemote cs r (with, errorval) command params fields = do
 	s <- git_annex_shell cs r command params fields
 	case s of
-		Just (c, ps) -> liftIO $ with c ps
+		Just (c, ps) -> with c ps
 		Nothing -> errorval
 
 {- Checks if a remote contains a key. -}
@@ -100,14 +100,14 @@ inAnnex r k = do
 	showChecking r
 	onRemote NoConsumeStdin r (runcheck, cantCheck r) "inannex" [Param $ serializeKey k] []
   where
-	runcheck c p = dispatch =<< safeSystem c p
+	runcheck c p = liftIO $ dispatch =<< safeSystem c p
 	dispatch ExitSuccess = return True
 	dispatch (ExitFailure 1) = return False
 	dispatch _ = cantCheck r
 
 {- Removes a key from a remote. -}
 dropKey :: Git.Repo -> Key -> Annex Bool
-dropKey r key = onRemote NoConsumeStdin r (boolSystem, return False) "dropkey"
+dropKey r key = onRemote NoConsumeStdin r (\f p -> liftIO (boolSystem f p), return False) "dropkey"
 	[ Param "--quiet", Param "--force"
 	, Param $ serializeKey key
 	]

RemoteDaemon/Transport/Tor.hs

@@ -69,7 +69,7 @@ server ichan th@(TransportHandle (LocalRepo r) _) = go
 				)
 			unless ok $ do
 				hClose conn
-				warningIO "dropped Tor connection, too busy"
+				liftAnnex th $ warning "dropped Tor connection, too busy"
 	
 	handlecontrol servicerunning = do
 		msg <- atomically $ readTChan ichan