Fix direct mode getKeysPresent false positive & also sped up direct mode unused and unannex

unused: In direct mode, files that are deleted from the work tree are no longer incorrectly detected as unused.

Direct mode `git annex info` slows down a bit due to more stringent
checking, but not by a lot.

Command/Info.hs

@@ -281,7 +281,7 @@ cachedPresentData = do
 	case presentData s of
 		Just v -> return v
 		Nothing -> do
-			v <- foldKeys <$> lift getKeysPresent
+			v <- foldKeys <$> lift (getKeysPresent InRepository)
 			put s { presentData = Just v }
 			return v