Unfortunately help page is misleading here. What you need is to add several Content roots for the folders that should be part of your project. If you want to exclude something under these roots, click 'Exclude'.
Thanks for the quick reply. So does adding Resource roots do anything other than changing folder color? It would be a nice enhancement for it to be used to include sources folders which makes it cleaner than excluding a bunch.
Actually resource roots should correspond to the HTTP server configuration. This allows IDE to complete and validate paths for included resources, e.g. <img src="/some/path/a.png"/>.