(Think of these as temporary folders where you get organized.) In these folders you can add and delete files without worrying. The effects and generator folders are where you want to organize your VSTs. The plugin database structure works like this. (Also automatically including a thumbnail image of the VST for you!) However, once learned, the approach is simple, and actually allows you to structure your Generators and Effects in your own way. I remember when first updating to FL Studio 12, it looked amazing! – But the folder structure really got me confused it was a new approach.
This post was written while using FL Studio version 12.2 The New Plugin Database Structure