Improve shutdown due to --time-limit, especially for fsck

* Perform a clean shutdown when --time-limit is reached.
  This includes running queued git commands, and cleanup actions normally
  run when a command is finished.
* fsck: Commit incremental fsck database when --time-limit is reached.
  Previously, some of the last files fscked did not make it into the
  database when using --time-limit.

Note that this changes Annex.addCleanup hooks, to run after --time-limit
expires. Fsck was using such a hook to clean up after a
--incremental-schedule, and that shouldn't run when --time-limit exipires
it. So, instead, moved that cleanup code to be run by cleanupIncremental.
Resulted in some data type juggling.

Limit.hs

@@ -13,6 +13,7 @@ import qualified Utility.Matcher
 import qualified Remote
 import qualified Backend
 import Annex.Content
+import Annex.Action
 import Annex.UUID
 import Logs.Trust
 import Annex.NumCopies
@@ -271,6 +272,7 @@ addTimeLimit s = do
 		if now > cutoff
 			then do
 				warning $ "Time limit (" ++ s ++ ") reached!"
+				shutdown True
 				liftIO $ exitWith $ ExitFailure 101
 			else return True