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.

Annex/Content.hs

@@ -97,29 +97,29 @@ inAnnex key = inAnnexCheck key $ liftIO . doesFileExist
 inAnnexCheck :: Key -> (FilePath -> Annex Bool) -> Annex Bool
 inAnnexCheck key check = inAnnex' id False check key
 
-{- inAnnex that performs an arbitrary check of the key's content.
- -
- - When the content is unlocked, it must also be unmodified, or the bad
- - value will be returned.
- -
- - In direct mode, at least one of the associated files must pass the
- - check. Additionally, the file must be unmodified.
- -}
+{- inAnnex that performs an arbitrary check of the key's content. -}
 inAnnex' :: (a -> Bool) -> a -> (FilePath -> Annex a) -> Key -> Annex a
 inAnnex' isgood bad check key = withObjectLoc key checkindirect checkdirect
   where
 	checkindirect loc = do
 		r <- check loc
 		if isgood r
-			then do
-				cache <- Database.Keys.getInodeCaches key
-				if null cache
-					then return r
-					else ifM (sameInodeCache loc cache)
-						( return r
-						, return bad
-						)
+			then ifM (annexThin <$> Annex.getGitConfig)
+				-- When annex.thin is set, the object file
+				-- could be modified; make sure it's not.
+				-- (Suppress any messages about
+				-- checksumming, to avoid them cluttering
+				-- the display.)
+				( ifM (doQuietAction $ isUnmodified key loc)
+					( return r
+					, return bad
+					)
+				, return r
+				)
 			else return bad
+ 
+	-- In direct mode, at least one of the associated files must pass the
+	-- check. Additionally, the file must be unmodified.
 	checkdirect [] = return bad
 	checkdirect (loc:locs) = do
 		r <- check loc
@@ -750,9 +750,17 @@ isUnmodified key f = go =<< geti
 	cheapcheck fc = anyM (compareInodeCaches fc)
 		=<< Database.Keys.getInodeCaches key
 	expensivecheck fc = ifM (verifyKeyContent RetrievalAllKeysSecure AlwaysVerify UnVerified key f)
-		-- The file could have been modified while it was
-		-- being verified. Detect that.
-		( geti >>= maybe (return False) (compareInodeCaches fc)
+		( do
+			-- The file could have been modified while it was
+			-- being verified. Detect that.
+			ifM (geti >>= maybe (return False) (compareInodeCaches fc))
+				( do
+					-- Update the InodeCache to avoid
+					-- performing this expensive check again.
+					Database.Keys.addInodeCaches key [fc]
+					return True
+				, return False
+				)
 		, return False
 		)
 	geti = withTSDelta (liftIO . genInodeCache f)