NiosI (and I'm hoping Nios2 based on Jesse's comment that I quoted) operates completely over the JTAG port without germs. nr myprog.srec downloads and runs myprog over jtag without germs.
It would be nice if n2r mynios2prog.srec worked the same way.
Here is a partial workaround using the fs2 debug console. You need to read "Getting Started" under help menu in the console.
n2c
openport altlpt1 //openport sld will work but lower performance
load srec mynios2prog.srec
//Basic run commands
step
go
halt
// read all registers
regs
// open a window for stdio
stdio window
If you turn on HW Trace you can get not only HW trace but minimal source level debugging as well
but you have to run nios2-elf-fs2symbols mynios2prog. A bug that seems common to most N2 tools is you must have a .elf file extension but the sample makefile produces a .out file. No fear, you can just copy myprog.out myprog.elf. Another anoyance is the .elf has to be in the same dir as your .srec so if you're using the sample makefile cp obj/myprog.out ./myprog.elf before generating the fs2 symbol file. (this out/elf bug happens with n2d as well)
The downside to operating over the jtag using fs2 console is that the 'stdio window' does not seem to function as it does with nios1 programs. (Altera? Anyone?)
Ken