For those who ordered Spartan 6 + ATSAM, here is the schematics and PCB layout. As mentioned earlier, this board is never assembled or tested. There are some known issues with the physical boards distributed. The SUSPEND pin of the FPGA is left floating, and may cause problems during configuration (this is fixed in the published design though). The PROG_B pin needs a pull up which can be connected externally. KiCad design files for this board can be downloaded here.