code c++

You can use the JTAG conneciton as stdin/sdout, then for command prompt and printf.

You can't use the .txt file, unless you implement a filesystem with Nios and a NV memory device and I think you don't want to make such an effort.

I'd suggest to incorporate the script.txt file information into the code, assuming you don't need to modify it. This is ok if itt contains only configuration information to be read when the executable starts.