How to link the codes on Spree Github with the codes on Ruby on Rails spree ecommerce store

sorry if this questions are too simple. Just started to learn Ruby on Rails and Spree ecommerce.

Successfully installed the demo store according the the instructions here: http://ift.tt/U8mBUt , however, I don't quite understand how the source codes at the Github are linked to the sources codes on the Ruby on Rails spree ecommerce store. The directories are pretty different from each other. For example, spree source codes have "/API", "/backend", "/core", etc... while the ruby on rails spree ecommerce store has "/app", "/bin", "/config", etc...

I know the ruby on rails auto generates some codes. But how the two correlated with each other? Say, some codes at Spree ecommerce are updated, what to do to update the Spree store?

thank you very much!