After many hours of struggles getting the DE0-Nano-Soc / Atlas-SoC kit working fully between the FPGA and the Linux system, I've decided I want to share the framework I'm using:
https://github.com/sveinse/de0-nano-soc The framework is based on the GHRD shipped with the kit, and is using the simple one-file Makefile from Altera. Plus some additional improvement. One of the features with this framework is that it allows development of the FPGA system independent of the software compilation with dedicated handoffs between the stages. It also includes a Linux tool, mksdcard, to create fully bootable SD-Cards from these handoff-files. Nothing fancy, but it collects the development workflow from building the FPGA image to compiling the software. The project also provides an update board file (DTAppend statement) for the newer kernels. A current problem is that the included board files are outdated. If the board is attempted run as-is with the recent Altera CycloneV kernels, it does not work completely. Both ethernet, mmc and the hps2fgpa_bridges haven't been functioning. This I believe has been fixed now. Enjoy. I'm very happy if I get any comments or feedback.