Darren:
For those just getting familiar with things, we normally suggest using the Linux / Zynq design first. It's a little easier to use and interact with the AD9361 on either the fmcomms2 or 3.
Once you are familiar with the AD9361, and the linux GUI, it's much easier to move to the no-os design on either Zynq or a fabric only solution.
As for the HDL - the source files were hand written. There isn't a machine generated file that I'm aware of - Rejeesh would know for sure.
- Robin