I have an Atmel ATSAMA5D3 eval board, and it appears to have u-boot and Yacto Linux pre-installed. Does anybody know how to tell u-boot to load an operating system from the SD card?

I have looked at various loader options, but all of them require a magic word.

Also, arm-none-eabi-gcc is the correct toolchain, correct?

These are not really FreeRTOS questions...you will have much better response to the booting question if you ask it on an Atmel forum, where everybody reading the text will be using the same or similar chips. With regards to GCC, then if you have the Launchpad GCC (https://launchpad.net/gcc-arm-embedded) then it doesn't mention Cortex-A. I think the Cortex-A versions of GCC I have used have originated from CodeSourcery, but check the list of supported architectures before downloading (https://www.mentor.com/embedded-software/sourcery-tools/sourcery-codebench/platforms/). Linaro might have something suitable too, if they have any unhosted compilers (https://releases.linaro.org/14.04/components/toolchain/binaries/)