Commands.jar is an external jar designed for the Orpheus external CommandLoader system. It contains an example of how one would make use of the system, and the commands it contains are based on enumerated commands.
An external CommandLoader is the fancy terminology for Orpheus' new command system. The idea is that commands are loaded from an external jar file in order to allow for them to be retroactively updated. All that means is, when you update the commands, you can see the updates on the server without a restart. All you have to do is use the developer command!
Well, that's not a problem! It can be disabled easily! Simply head over to your ServerConstants and turn off the setting that enables the usage of the command loader! That's it!
Thanks to angelsl for the idea!