Building NIOS2 Applications using command line

It depends on the scope of what you're trying to test. Are you verifying just the logic in the software, or the hardware as well?

For just the software I suppose you could use a similar GNU compiler/linker suite that produces a x86 target in a regression test harness. For such a test it would be worth implementing a Hardware Abstraction Layer to allow stubs to replace the real I/O.

If you're using ATE to test the hardware, and need to run the image there is probably a "very hacky" way of automating the running of the NIOS environment. You could use Spy++ to determine the window classes and WM_COMMAND messages fired for specific menu commands. Then use FindWindow and SendMessage to determine the window handle and fire the menu commands in your test harness app'. Be careful with using Spy++, it can hang your machine.

I've just experimented with this -> the window class is SWT_Window0 (child windows also have this, but no menu handle), and the "Run" command ID is 274.