Open up app folder, it's a basic project folder for DooPHP. Every new Doo app you create uses the same project structure.

In a project folder you have:

global - put your javascript, images, css, flash here.
protected - your DooPHP app script files.

In protected you have:
cache - place to store your cache files.
class - put your useful 3rd party PHP class here to be used with DooPHP
config - the 3 configuration files are here: common, routes, database configs.
controller - Your Controller classes here. There's a MainController by default.
model - Your Model classes here.
plugin - there's a file called template_tags.php for you to add features to the View
view - Your Html template files here.
viewc - Consist of compiled template files.

Most of the time, you would be working with 4 folders, model, view, controller and config.