Build the bootloader by following the instructions in the readme from the github repository:

https://github.com/gsteiert/uf2-samdx1

The .elf file can be loaded using openocd.  I suggest using the MAX32625PICO# board. It is a very nice low cost debug adapter:  

https://octopart.com/search?q=max32625pico&start=0

After the bootloader is loaded, the board should appear as a drive named HELPERBOOT:

This github repo includes the fpga_helper board:

https://github.com/gsteiert/circuitpython

Follow the same build instructions as the Adafruit repo:

https://learn.adafruit.com/building-circuitpython?view=all

Just make sure you build BOARD=fpga_helper

After the build completes, you can drag-n-drop the firmware.uf2 files onto the HELPERBOOT drive.  

After loading the firmware, the board will reset and a CIRCUITPY drive will appear.

Copy the files found here to the CIRCUITPY drive:

https://github.com/gsteiert/FPGA-helper/tree/master/circuitpy

After copying the files the drive should look like this:

After you reset the board, it will first run boot.py and put the results in boot.txt.

If you have attached a Qwiic NFCPROM, you will see results like this:

Adafruit CircuitPython 4.0.0-alpha.1-4-gf09537b-dirty on 2018-10-01; Steiert Solutions FPGA Helper with samd21e18
boot.py output:
bytearray(b'\xe1@@\x05\x03\x14\xd1\x01\x10U\x03dei.steiert.net\xfe\xffCARD')

If nothing is connected the results will look more like this:

Adafruit CircuitPython 4.0.0-alpha.1-4-gf09537b-dirty on 2018-10-01; Steiert Solutions FPGA Helper with samd21e18
boot.py output:
Traceback (most recent call last):

  File "boot.py", line 7, in <module>

OSError: [Errno 5] Input/output error

 After finishing boot.py, it will run main.py and the LED will fade through different colors.