Sencha cmd causing app to pull resources from /build

I have generated an app skeleton using "sencha generate". When I delete the /build dir everything stops working. Why is Sencha-cmd authoring my bootstrap.* files to point to resources in /build?

I am in the process of figuring out what directories and files to check into SVN and am wondering why I need /build since this dir should only contain generated "deploy-able" artifacts not needed for development.