Your website URL should be mapped to the "webroot" folder. All files within this folder are accessible via an http request on your domain. Any files that are included server side should go into the "includes" folder.
atomantic/HTML5-Site-Template
A template for creating a new HTML5 website (folder structure and base files) -- this project is mainly a hub for students of Adam Eivy's Web Development classes at Seattle Central Community College but is available to anyone who wishes to join in creating a universally usable foundation for an html5 site template. Please make suggestions for additions/modifications or join the project before forking :)