Flash Help!

You don't really need to rely on the Nios II's IDE to program the FLASH. It just means that you have more work to do. The easiest option is to make a program that does know how to write to your FLASH device, put the code/data you want flashed in the program as an array (c initializer) then download your program to RAM through the JTAG interface and have your code FLASH the data from the array into the FLASH.

This requires two big steps. Getting your code/data into a binary format and getting that binary data into a c initializer. objcopy is very useful for getting the code into a binray format and I find that perl (or other scripting languages) are easy to use to create a c-initializer of the binary data.