Following this guide:
in part 3: Building and Using Host Applications they talk about working with files on the pi that are generated (I assume) through Simplicity Studios.
"The Linux host is loaded with the spi-server application, the ip-driver-app, and the top-level host application"
How do I generate these applications?
Those applications come with our stack. If you have transferred the whole stack over to the raspberry pi, you can follow the instructions on step 3 there and build the applications.