IDE generated files

We have a design using a Nios II processor within a Cyclone FPGA, along with interface to external Flash, SRAM, and off-board logic. All the modules have been built up properly through SOPC Builder. Once IDE was invoked from SOPC Builder, we were trying to obtain two files, system.h and generated.x. However, our software engineer kept running into error messages through a simple build. Thus, we would like to know how to integrate our software within our designs. Here are our software environment needs:

1) commercial RTOS needs a modified generated.x file

2) build environment is command-line

3) need to created generated.x without target software