If you find your folders a little crowded, you can add subfolders.

If you have an item, Sword, in your item folder, you can add a new folder to your item folder, and call it anything you want. For this example, I'll just add a folder called weapons.

Everything within your Sword.js will remain untouched, but in your mod.js, change the line

mod.addItem("Sword.js", "normal");

to this:

mod.addItem("weapons/Sword.js", "normal");