MickMake posts about programming Microchip/Atmel SAM series chips without an integrated development environment (IDE).

The Atmel SAM MCUs are a step up from the old AVR series. Atmel provide a range of them targeted towards different applications. Besides running an ARM core they also have multiplexed serial comms, called SERCOM, allowing you to assign functions to different pins. They’re a pretty neat chip.

However, if you’ve ever designed a board yourself, like (the one above that) I designed for a customer, the MCU won’t of course contain any bootloader, which is a requirement if you want to use an IDE like Arduino or Eclipse.

With the method presented, you can choose to burn a bootloader and then use one of those IDEs, or just keep using the method to develop your code.

See the whole step by step process on mickmakes.com.