The limitation is that there is only one on-board clock on the NiteFury/Acorn, a 200Mhz DDR clock.
What about the 90Mhz clk U10 3V3 on page 6 in the schematic connected to pin V22 on the Artix-7 can that be used as a stand alone clk, or is th 200MHz DDR clk the only option?
If you notice this pin is labeled: IO_L3N_T0_DQS_EMCCLK_14_0
EMCCLK is a clock pin specified for "Configuration Logic" I don't believe it is also a clock capable pin like others which will say MRCC or SRCC for example.
Looking more closely at the the DDR 200Mhz clock, you can absolutely use that as a standard clock, I may just not fully understood what I was doing at the time with the MIG7 DDR3 controller IP core. It may not be possible to use the DDR3 core at the same time with the using the 200Mhz clock with other stuff but looking at it again I see that the DDR clock comes in on MRCC clock pair.
Just be sure you know it comes in as a differential clock pair, you need to buffer this with the appropriate clock buffer options in either the clocking wizard if you use block view or instantiate the correct clock buffers in your HDL.
Here this will be your friend and enemy:
https://www.xilinx.com/support/documentation/user_guides/ug472_7Series_Clocking.pdfAlso one thing I did mean and I know is impossible is driving PCIe off of this as a root complex without an external clock. The PCIe connection on the M.2 goes specifically to phys designed for the PCIe or similar high speed interface. This INCLUDES the PCIe clock connection, which is ONLY an input for the clock, this pair can not be driven and as such if you want to use this as a root complex you'll need a board with an M.2 to PCIe connector with the related power supply (3.3V) and HCST clock driver for both the nite-fury/sqrl and the endpoint PCIe slot. I was working on designing a board for JUST that case, but got side-tracked by another FPGA project
Also I noticed that post by futaris and well... My thunder was stolen heh. So I figured I'd wait to see where that goes and maybe give that litex core a try, although they have a PCIe ENDPOINT not a ROOT COMPLEX! So less fun IMO
Anyway good luck and let us know how you make out!