Make it works with YFS.
Make it works with YFS.

1. update the declaration of clockManager.
2. add an initial value in clockManager (this introduces non-determinism, which
   is required by applications like YFS.
3. fixed a bug: incorrect use 10^5 and 10^9.
4. use clockManager in TimeClock/TimedWait if epoch_mode is set.

columbia/xtern,hemingcui/xtern_with_paxos,columbia/xtern,hemingcui/xtern_with_paxos,columbia/xtern,columbia/xtern,hemingcui/xtern_with_paxos,hemingcui/xtern_with_paxos,columbia/xtern,columbia/xtern,hemingcui/xtern_with_paxos