Q: How do I make UAR run bungee commands?
A: In order to use bungee commands with UltimateAutoRestart you need the passthrough plugin installed on your bungee server. After that, simply put "[bungee]" in front of the command, the command will then be executed through the bungee console when the server restarts. You can find an example on how to send players to a specific server by viewing the default configuration. You do not put the bukkit plugin inside your bungee plugins folder.
Q: How do I make UAR run interval-based bungee commands?
A: Simply add "[bungee:x]" in front of the bungee command (x being the amount of seconds before the restart happens). For example "[bungee:5] send skyblock lobby" will send all skyblock players to the lobby server 5 seconds before the restart. Please read the next Q&A as well.
Q: My bungee commands do not always work, why?
A: This is a bungee messaging channel limitation and there's nothing I (as the developer of the plugin) can do something about. In order for bungee commands to execute there needs to be an online player on the server that UAR (not bungee version) is installed on.