fix flush of a closed file handle

Avoids displaying warning about git-annex restage needing to be run in
situations where it does not.

Closing a handle flushes it anyway, so no need for an explict flush. The
handle does get closed twice, but that's fine, the second one does nothing.

Sponsored-by: Dartmouth College's DANDI project

Git/UpdateIndex.hs

@@ -160,7 +160,6 @@ refreshIndex repo feeder = bracket
 
 	go (Just h, _, _, pid) = do
 		let closer = do
-			hFlush h
 			hClose h
 			forceSuccessProcess p pid
 		feeder $ \case