I've completed basic windows configurations for PlatformIO and Arduino IDE. In the Arduino IDE, code compilation, upload, and bootloader burning are all working.

I'm now able to debug code from within PlatformIO, which is a lot more streamlined than from within Microchip Studio (you do lose a few small features). See https://github.com/fortytwosystems/platform-atmelsam for the platform files. Currently, the following must be specified in the platformio.ini file:

[env:fortytwo_mega]
platform = https://github.com/fortytwosystems/platform-atmelsam.git
platform_packages = 
    framework-arduino-samc-fortytwo @ https://github.com/fortytwosystems/ArduinoCore-samc
    framework-cmsis-microchip @ https://github.com/fortytwosystems/ArduinoModule-CMSIS-Microchip
    tool-bossac-samc @ https://github.com/fortytwosystems/BOSSA#pio-windows
board = fortytwo_mega
framework = arduino

I'm hoping to clean things up in the following weeks by publishing the packages to the PlatformIO registries. Until I ship a significant number of boards and get support from the official PlatformIO repo, I will have to use the fortytwosystems github link for the platform variable.

I've finished my modifications to BOSSA by adding all chips in the SAMC21 line to the Devices.cpp file. I need to compile bossac for mac and linux systems still.