print a warning message when garbage is received from configlist

Messages.hs

@@ -23,6 +23,7 @@ module Messages (
 	showEndResult,
 	showErr,
 	warning,
+	warningIO,
 	fileNotFound,
 	indent,
 	maybeShowJSON,
@@ -158,6 +159,12 @@ warning' w = do
 		hFlush stdout
 		hPutStrLn stderr w
 
+warningIO :: String -> IO ()
+warningIO w = do
+	putStr "\n"
+	hFlush stdout
+	hPutStrLn stderr w
+
 {- Displays a warning one time about a file the user specified not existing. -}
 fileNotFound :: FilePath -> Annex ()
 fileNotFound file = do

Remote/Git.hs

@@ -161,8 +161,15 @@ tryGitConfigRead r
 			=<< liftIO (try a :: IO (Either SomeException Git.Repo))
 
 	pipedconfig cmd params =
-		withHandle StdoutHandle createProcessSuccess p $
-			Git.Config.hRead r
+		withHandle StdoutHandle createProcessSuccess p $ \h -> do
+ 			fileEncoding h
+			val <- hGetContentsStrict h
+			r' <- Git.Config.store val r
+			when (getUncachedUUID r' == NoUUID && not (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!"
+			return r'
 	  where
 		p = proc cmd $ toCommand params