Integrated into the current cgminer version via the A1 SPI driver today. Some thoughts:

HW_RESET via Pi's GPIO needs elevated privileges and is hardware specific, so I prepared a separate binary for that. Currently HW_RESET is only done once at start, hopefully doing it this way won't be a problem.

The reference board doesn't really have any kind of detection mechanism other than probing the SPI bus, so the board selector is stubbed out.

Also, I was thinking of modifying the set_pll code so that the fb_div never drops below 100, would this be of use?

I'm not sure if these changes would be accepted into the main cgminer branch, since they are not for a commercial product, but if there is any interest, I'd be happy to share the code.