Until recently, CSS and JavaScript files that you create via Structure > CSS and Structure > JavaScript always appeared at the root of your site. Since we display them separately and manage them in the CMS, there isn't any real need to put them off in separate folders.

However, this is sometimes a pain when you're converting an existing design, which typically will put the CSS and JavaScript files in folders of their own.

Now you can specify what folder these files appear in. From either the CSS or the JavaScript admin page, just choose Change Folder from the menu that appears when you click the Actions button.

Note that this is entirely separate from uploading CSS or JavaScript files via Content > Images & Files. That approach is best for library files, since you don't need to edit them, but for files that you do need to be able to edit, it is easier to store them in the CMS.