fix inode cache consistency bug when a merge unlocks a present file

Since the file was present and locked, its annex object was not in the
inode cache. So, despite not needing to update the annex object when the
clean filter is run on the content by git merge, it does need to record the
inode cache of the annex object. Otherwise, the annex object will be
assumed to be bad, since its inode is not cached.

Annex/Content.hs

@@ -544,12 +544,16 @@ data FromTo = From | To
  -}
 linkAnnex :: FromTo -> Key -> FilePath -> Maybe InodeCache -> FilePath -> Annex LinkAnnexResult
 linkAnnex _ _ _ Nothing _ = return LinkAnnexFailed
-linkAnnex fromto key src (Just srcic) dest = 
+linkAnnex fromto key src (Just srcic) dest = do
-	ifM (liftIO $ doesFileExist dest)
+	mdestic <- withTSDelta (liftIO . genInodeCache dest)
-		( do
+	case mdestic of
-			Database.Keys.addInodeCaches key [srcic]
+		Just destic -> do
+			cs <- Database.Keys.getInodeCaches key
+			if null cs
+				then Database.Keys.addInodeCaches key [srcic, destic]
+				else Database.Keys.addInodeCaches key [srcic]
 			return LinkAnnexNoop
-		, ifM (linkOrCopy key src dest)
+		Nothing -> ifM (linkOrCopy key src dest)
 			( do
 				thawContent $ case fromto of
 					From -> dest
@@ -557,7 +561,6 @@ linkAnnex fromto key src (Just srcic) dest =
 				checksrcunchanged
 			, failed
 			)
-		)
   where
 	failed = do
 		Database.Keys.addInodeCaches key [srcic]