v6: Fix database inconsistency

That could cause git-annex to get confused about whether a locked file's
content was present, when the object file got touched.

Unfortunately this means more work sometimes when annex.thin is set,
since it has to checksum the file to tell if it's still got the right
content.

Had to suppress output when inAnnex calls isUnmodified, otherwise
"(checksum...)" would be printed in places it ought not to be,
eg "git annex get" could turn out not need to get anything, and
so only display that.

This commit was sponsored by Ole-Morten Duesund on Patreon.

Messages.hs

@@ -16,6 +16,7 @@ module Messages (
 	showSideAction,
 	doSideAction,
 	doQuietSideAction,
+	doQuietAction,
 	showStoringStateAction,
 	showOutput,
 	showLongNote,
@@ -111,11 +112,27 @@ doSideAction :: Annex a -> Annex a
 doSideAction = doSideAction' StartBlock
 
 doSideAction' :: SideActionBlock -> Annex a -> Annex a
-doSideAction' b a = do
-	o <- Annex.getState Annex.output
-	set $ o { sideActionBlock = b }
-	set o `after` a
+doSideAction' b = bracket setup cleanup . const
   where
+	setup = do
+		o <- Annex.getState Annex.output
+		set $ o { sideActionBlock = b }
+		return o
+	cleanup = set
+	set o = Annex.changeState $ \s -> s { Annex.output = o }
+
+{- Performs an action, suppressing all normal standard output,
+ - but not json output. -}
+doQuietAction :: Annex a -> Annex a
+doQuietAction = bracket setup cleanup . const
+  where
+	setup = do
+		o <- Annex.getState Annex.output
+		case outputType o of
+			NormalOutput -> set $ o { outputType = QuietOutput }
+			_ -> noop
+		return o
+	cleanup = set
 	set o = Annex.changeState $ \s -> s {  Annex.output = o }
 
 {- Make way for subsequent output of a command. -}