My own made CommandAPI for Bukkit Plugins Has multiple functions such as:
- multiple commands in one class
- automated help menu
- automated permission checks
- automated arg flags
- simple to use
- no editing of plugin.yml required
For an example project see https://github.com/TheJeterLP/CommandAPIExample
For including into your project use the Maven Shade plugin. Since I dont own a Maven repo, clone this project into your IDE and build it. After that everything should work and it gets shaded into your plugin when you build it and have the pom.xml file setup correctly.