rppolicy,
I suggest two things:
Check out app note# 350 on migrating Nios to Nios II. I know you are writing about a new design, but this document talks about the differences between legacy SDK mode and eclipse/HAL.
Next, I would like to make one thing clear: With Nios II, we wanted to deliver the SDK support just as it was for Nios I -- this way you lose nothing!! We realize that many people writing simple software or those who prefer a command-line world will prefer the SDK. However, as our performance and capabilities increase, please realize that the move to an IDE is for the common good in the long run: lots of software developers have been asking for this for some time because they wish to port more platform independent code to Nios (which is where the HAL comes in). Toss in RTOS/OS support, and a more complex software dev environment is in order.
Anyways, sorry for all that text above. I suggest one thing for the GERMS monitor -- I am a bit confused by this talk of hex files and such -- you should only need to enable GERMS by:
1. Adding an on-chip memory from the "Legacy Components" folder of SOPC Builder
2. Making this memory 2K bytesx32
3. Specifying GERMS for the contents of memory
4. Connect CPU instruction/data masters to the memory, and setting the boot address to it
5. Enabling legacy SDK support as you have already done.
Last, please note that we do not "officially" support the Nios II /f core with legacy mode. This is due to the different data cache architecture compared to Nios I. We have found that most code will work, but cannot guarantee that all calls to C libraries will keep things like volatile pointers as they should. As I said though, most things will work
http://forum.niosforum.com/work2/style_emoticons/<#EMO_DIR#>/smile.gif