The idea is to make existing arduino programs "just run", so the lowlevel i2c commands need to get implemented using i2c-dev, the spi commands with spi-dev, etc. That also means that under the hood you will need to use devicetree overlays to set pinmux, initialize hardware, etc. Depending on how much you want to tackle in this project, you might even need to write some helper drivers in the kernel to expose more things to sysfs or have a better suited device node.
regards,
Koen