SAMG55 - bootloader tools
After some research, I tracked down a copy of the zip file (20831 bytes) for Atmel Application Note AT09002 which was stored in the Wayback Machine (archive.org) on 1st August 2017:

Atmel-42305-SAM-I2C-SPI-Bootloader_ApplicationNote_AT09002.zip

It contains the Python tool hex2fy.py and config files which you mentioned.

That's the latest version which I could find archived there.