Thank you for the pointers. I read the text, but it was not really applicable. I don't know why I didn't think of it before, but I opened the prompt and built the project using "make all", omitting the -s switch, I piped the output to a file, and rebuilt my own makefiles.
Next issue on the table is the NIOS-II IDE. It appears that it is impossible (ok .. ok .. very difficult ) to create a project and compile files which are OUTSIDE the project directory. I could use Visual Studio as an editor, but I really like the integrated debugging facilities in the NIOS-II IDE.
Any ideas?