The webroot directory structure is a duplicated from the /concrete directory to allow you to modify/change the behavior of the core. The core is the /concrete directory and the files there can be overridden by using the corresponding directory in the webroot. It also allows the C5 /concrete directory to be updated with future releases and still keep all your modifications/changes in tact. Example: Say your want to modify the "default theme". You copy the /concrete/themes/default to the /themes folder and modify it. Since there is a theme located in webroot called default, concret5 will ignore the core /concrete/themes/default and use your modified theme in your webroot. Make sense?