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That is what I do right now, I just control and parametrize my application using the nios2-terminal via jtag-uart, but my customer prefers a solution without having to install the nios sdk.
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If you want to avoid installing NIOS EDS, or Quartus, use one of the JTAG interfaces that support scripting. They are available when you install the Quartus Programmer.
Virtual JTAG is the more powerful one, but it is also the one that requires more work and it is rather slow. You might prefer to use the In-System probes or memory editor.
It is also possible to use your own application to control the USB blaster interface, and then avoid the need of installing any Quartus/Altera software at all. This is not documented by Altera, but the information is available on the net.
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