fix --all to include not yet committed files from the journal

Fix bug caused by recent optimisations that could make git-annex not see
recently recorded status information when configured with
annex.alwayscommit=false.

This does mean that --all can end up processing the same key more than once,
but before the optimisations that introduced this bug, it used to also behave
that way. So I didn't try to fix that; it's an edge case and anyway git-annex
behaves well when run on the same key repeatedly.

I am not too happy with the use of a MVar to buffer the list of files in the
journal. I guess it doesn't defeat lazy streaming of the list, if that
list is actually generated lazily, and anyway the size of the journal is
normally capped and small, so if configs are changed to make it huge and
this code path fire, git-annex using enough memory to buffer it all is not a
large problem.

CmdLine/Seek.hs

@@ -276,7 +276,7 @@ withKeyOptions' ko auto mkkeyaction fallbackaction worktreeitems = do
 		let discard reader = reader >>= \case
 			Nothing -> noop
 			Just _ -> discard reader
-		let go reader = liftIO reader >>= \case
+		let go reader = reader >>= \case
 			Just (k, f, content) -> checktimelimit (discard reader) $ do
 				maybe noop (Annex.Branch.precache f) content
 				keyaction Nothing (SeekInput [], k, mkActionItem k)
@@ -373,7 +373,7 @@ seekFilteredKeys seeker listfs = do
 	liftIO $ void cleanup
   where
 	finisher mi oreader checktimelimit = liftIO oreader >>= \case
-		Just ((si, f), content) -> checktimelimit discard $ do
+		Just ((si, f), content) -> checktimelimit (liftIO discard) $ do
 			keyaction f mi content $ 
 				commandAction . startAction seeker si f
 			finisher mi oreader checktimelimit
@@ -384,7 +384,7 @@ seekFilteredKeys seeker listfs = do
 			Just _ -> discard
 
 	precachefinisher mi lreader checktimelimit = liftIO lreader >>= \case
-		Just ((logf, (si, f), k), logcontent) -> checktimelimit discard $ do
+		Just ((logf, (si, f), k), logcontent) -> checktimelimit (liftIO discard) $ do
 			maybe noop (Annex.Branch.precache logf) logcontent
 			checkMatcherWhen mi
 				(matcherNeedsLocationLog mi && not (matcherNeedsFileName mi))
@@ -591,9 +591,9 @@ notSymlink :: RawFilePath -> IO Bool
 notSymlink f = liftIO $ not . isSymbolicLink <$> R.getSymbolicLinkStatus f
 
 {- Returns an action that, when there's a time limit, can be used
- - to check it before processing a file. The IO action is run when over the
- - time limit. -}
-mkCheckTimeLimit :: Annex (IO () -> Annex () -> Annex ())
+ - to check it before processing a file. The first action is run when over the
+ - time limit, otherwise the second action is run. -}
+mkCheckTimeLimit :: Annex (Annex () -> Annex () -> Annex ())
 mkCheckTimeLimit = Annex.getState Annex.timelimit >>= \case
 	Nothing -> return $ \_ a -> a
 	Just (duration, cutoff) -> return $ \cleanup a -> do
@@ -602,6 +602,6 @@ mkCheckTimeLimit = Annex.getState Annex.timelimit >>= \case
 			then do
 				warning $ "Time limit (" ++ fromDuration duration ++ ") reached! Shutting down..."
 				shutdown True
-				liftIO cleanup
+				cleanup
 				liftIO $ exitWith $ ExitFailure 101
 			else a