Building for Nios without using the Nios II command shell

Hi All,

I am currently automating a rather complex build system and need to be able to build for multiple targets (including the much hated Xilinx :) ).

I am having an issue where I need to have cygwin installed for other builds on the same system but get the following error when I launch a Nios II command shell

Removing old PATH, because a copy of
. cygwin1.dll was found at: 
.     /cygdrive/c/cygwin/bin/cygwin1.dll
. You can remove or rename it to avoid conflict.

This resets my Path and stops me picking up some tools that are not in the build directory. Platform is windows :( but I have no choice in this.

From what I can see the only solution is to rename my current install of cygwin (something I don't want to do). Does anyone know another way around this?

or

does anyone know how I can build for Nios without using the nios II command shell? i.e use normal windows cmd shell and set up any variables I require?

thanks,

G