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/Unused.hs

@@ -71,7 +71,9 @@ checkUnused = chain 0
 		return []
 	findunused False = do
 		showAction "checking for unused data"
-		excludeReferenced =<< getKeysPresent
+		-- InAnnex, not InRepository because if a direct mode
+		-- file exists, it is obviously not unused.
+		excludeReferenced =<< getKeysPresent InAnnex
 	chain _ [] = next $ return True
 	chain v (a:as) = do
 		v' <- a v