https://github.com/PocketMine/ExamplePlugin they have to be compressed into phar archives though using DevTools (https://github.com/PocketMine/DevTools)
Please don't tell me that's the plugin. https://github.com/PocketMine/ExamplePlugin/blob/master/plugin.yml
PHAR is like a php version of a java archive (JAR). You put your code in a PHAR along with plugin.yml, much like bukkit plugins. All the data of the plugin (commands, permissions, etc.) is contained in plugin.yml