You can now run bungee commands, the passthrough plugin is required to be installed on your bungee server in order for this to work. Read through the resource page to find out how to use this new feature, there's also a detailed example in the default configuration.
There is now a 3 second delay between each bukkit command, this change has been made so bungee has time to react in case you have bungee commands configured.
The actionbar handler has been changed to a more efficient one.