You have the option of processing the entire site, or having the Builder scan the site, and then present you with the opportunity to select which portions of the site you want processed.
If you click on Index selected items the Builder will scan the entire site for files, and then provide you with the opportunity to select which ones should and should not be processed, as well as placed into the site map.
If you click on Index whole site the Builder will scan and process the entire site.