In Site Definition, one can define the default folders or items that are created to a list on a site when the site is created using Lists-List-Data-Rows-Row-Field elements.
How to create folders that contain items, i.e., a hierarchy of folders containing items?
Cannot be done using current web's feature receivers since the list items do not yet exist when the features are activated.
Create a feature that moves the items into correct folders in the list. Activate this feature programmatically after the site is created.