replication: review fixes for replication_timeout

- Fix applier.cc/relay.cc dependencies. Relay/applier should not
  depend on box.cc. Add two separate flags to control timeout.
- Remove hardcoded REPLICATION_CFG_TIMEOUT.
- Fix replication_timeout value checking.

Follow up #2707

Signed-off-by: Roman Tsisyk <roman@tarantool.org>