TL;DR: I am trying to learn how to use the SAM4S Atmel chips with the Arduino IDE. I don't know how one goes about that. Would I have to write a custom bootloader? That seems hard!
I've been working on a small signal analysis project that I am seeking to commercialise down the road. I've initially developed with dsPIC33s but want to move to something compatible with the Arduino IDE to allow my technical end users to more easily tinker with the product. A key feature I require is decent FFT support, and my research shows me the Teensy is out ahead here because of the Cortex M4 chips having some sort of hardware specifically for these sort of operations.
One obvious road would be to use the Teensy 3.1 to develop, and to use the pre-programmed MINI54 chips from PJRC to make my product "Teensy compatible", and easy to use with the Arduino IDE. From what I have read, the MINI54 is just a bootloader. Would it then be feasible instead for me to use something like the SAM4S Cortex M4 chips from ATMEL and hook in USB directly to them for programming with the Arduino IDE? Or is there another step involved that I am missing here? Any guidance would be greatly appreciated as while I have some microcontroller experience, I am new to the world of USB programming/bootloaders/Arduino, etc. Back in my day you had a dedicated programmer and that was it!
Thanks!