libopencm3 VS atmel-software-package-samv7

Some of the vendor IDEs have the option to generate makefiles for a project. Depending on the processor, you could also opt out to a different system. A lot of the popular cortex-m stuff is supported by libopencm3.

You can also look at examples of HALs such as - libopencm3 (Though this is Cortex only) - RIOT OS (though this requires an RTOS)

Yeah by the looks of it I am going to have to expand my project do creating a portable driver interface as well. Abstracting hardware interfaces to create portable code is fairly common in embedded development. For example, libopencm3 does this and has great support for STM32 parts but very limited support for SAM parts.

TinyUSB or Libopencm3 are probably your best options (although check they support the SAME70).

that is fair. SPI isn't very portable across Arm cpu vendors because all peripherals are vendor specific, i.e. the registers will differ a lot and APIs reflect that. Finding common ground is hard unless using specifically designed portable libraries like https://github.com/libopencm3/libopencm3

I highly recommend the book "USB Design by Example", and reading the source to existing drivers. As for the SD card, it's a bit of a mixed bag. The SD card native mode protocol is technically only available under NDA, but it's been leaked and reverse engineered ad nauseum. If you want to take a look at existing solutions, I'd go through the legacy software package for SAM*7 processors, or the source for FreeRTOS. Leveraging either of these will get you there much quicker than trying to write everything from scratch, which is a MUCH bigger task than I think you realize.