How to classify plug-ins or modules?

As can be seen from the engine directory, many plug-ins of engine are placed in different directory.
But plugins we make must be in the Project\Plugins directory.
When I make more and more modules of the project, I hope my plug-ins are in the directory such as Project\Plugins\System, or the modules are in the Project\source\System. If modules or plugins are moved directly, engine will not find them. How to solve this problem?