I have Added option set to 'Product Display' content type to pick between 'assortment' or 'pick your own cookies' on the product page.

Added'Entity Reference View Widget' module, created an 'Entity Reference View' View to display 'Cookie flavours' taxonomy as part of the option set on the product page.
Added 'Conditional fields' module, and created dependency so that choosing 'pick your own cookies' makes the 'Entity reference view' with cookie flavours visible.
Added taxonomy terms (with images)

So, this brings us closer to the solution, but it is still not there. The 'Entity Reference View Widget' module is not fully working (https://drupal.org/project/entityreference_view_widget) - it should react when you click on the checkbox for the taxonomy terms, but it doesn't... and i Have been using stepper field module in place of check boxes.
This is the site i am working on
http://maximlesterdev.devcloud.acquia-sites.com/productdisplay/test
Can any one tell me how can i add all the taxonomy terms with different quantities into the cart.