This isn't an in-depth tutorial, just some notes I took since I was asked a few times how to modify/compile the bossac bootloader!

Download Latest Bootloader Code

The latest Arduino SAMD core is at https://github.com/arduino/ArduinoCore-samd

You can download a zip of the current snapshot or you can use git to clone the repository

Its better to do this than compile in the board-support-package location (e.g. C:\user\blah\local\arduino15) because you'll lose your changes if you update the BSP!

You'll need to have some basic command line compilation tools already installed like make - such as MSys or Cygwin (which we discuss here) or install make as a binary

Just make sure when you run make in a command line you get that it is looking for a makefile

Change into the bootloaders/zero directory

If you try to make all here and you get

fatal error: sam.h: No such file or directory

Make sure you've installed the Arduino SAM and SAMD packages through the board manager

Try make all again for success!

Before distributing, make sure to change the VID/PID in the makefile:

then run make clean and make all again to make fresh files

When you're done, you'll have two new files, samd21_sam_ba.hex and samd21_sam_ba.bin

Programming into an Arduino Zero w/EDBG

The easiest way to do this is just replace samd21_sam_ba.bin in C:\Users\ladyada\AppData\Local\Arduino15\packages\arduino\hardware\samd\1.6.4\bootloaders\zero (or where-ever the current version of your Arduino SAMD package is with the compiled samd21_sam_ba.bin

Launch the IDE, select Arduino Zero (programming port) from the Tools->Board menu, and Atmel EDBG as the Tools->Programmer

Then select Burn Bootloader

It only takes a few seconds to burn in the bootloader:

Feather M0 or Others

For this, you'll need to use an Atmel Studio or adalink setup, since you're using a J-Link or stlink.

Atmel Studio

If you're using Atmel Studio, install it

Plug in your Jlink and connect it to the SWD pins. OK now you have your debugger plugged in, its good to check that it works, select Device Programming

Under Tool make sure you can select J-Link

Select ATSAMD21G18A as the device, SWD as the interface and hit Apply

You can then Read the Device Signature. Make sure this all works before you continue!

If you are asked to update the J-Link firmware, its OK to do so now.

Next click on Memories in the left hand side

Next to the Flash (256 KB) section, click the triple-dots and select the hex bootloader file generated from the previous make all

Then click Program to program it in

If you don't have Windows you can install adalink

Then run adalink -v atsamd21g181 -p jlink -h samd21_sam_ba.hex

You can also check out https://learn.adafruit.com/programming-microcontrollers-using-openocd-on-raspberry-pi if you want hints on using OpenOCD directly!