The Plugin directory can contain Prism plugins, which modify or extend the functionalities of Prism when this project is active. You can use the same Prism plugins in this folder as in your Plugin directory in the Prism installation directory. Plugins in this directory are only available as long as this project is active.
You don't need to group plugins in this folder under "Apps", "Custom"... but make sure the self.pluginType variable in the plugin script identifies the type of Prism plugin. In your Prism installation directory you can find an example how to create a new Prism plugin.