• Theme
    • etc - come config files
    • layout - layout xml files that allow the blocks to be configured
    • template - the phtml template files

The maiin parks of a theme is made up of the layout files and the template files. The layout xml files define where the templates can be used with a tree structure and also defines which block classes are used with each template file. The templates are php files which contain mostly html although they do also have PHP.