Headless build for Nios II projects

You should be able to create the projects in Eclipse and then be able to use the generated makefile from the command line directly.

I typically skip that and use the software build tools directly when I want to implement automation of generating make files and automating the software downloading/execution. If you want to see an example of what I'm describing, take a look at the Qsys tutorial design and look for a shell script under the software directory. That script generates the necessary application and BSP make files, compiles the software, downloads the hardware, downloads the software, and opens a terminal window. You might not need to do all those steps but it should be easy to grab the stuff you need from it.