Learn about the "Code" folder where developers place their stuff and hide it for normal users.
The "folder" folder
Place all the default files for all folders except the root folder here. If you have a folder somewhere, the contents in this folder will be available there.
The "root" folder
Place all the default root files and folders you would like to include in your site in this folder.
The "API" folder
Create your custom JSON WEB API by placing JS files that will run server side in the #/API foider.