Hi GreateWhite.DK,
If you can find the source of the userland applications provided by the Microtronix installation, you will see a lot of examples there (under the directory user).
Baiscally you need to link all your .o files into a .bin file:
nios2-elf-gcc -msys-crt0=$(uClibc-CRT0) -r -d -o app.bin m1.o m2.o m3.o $(LDLIBS)
Then use the linking script provided by microtronix:
nios2-elf-ld -T elf2flt.ld -Ur -o app.elf app.bin
At last convert app.elf to FLT format:
elf2flt -s 16000 -o app.flt app.elf
These steps are quite confusing, but if you can find and use the rules.mak Microtronix provided in the user applications, all you need to do is some lines in the app Makefile:
include Rules.mak
all: app.flt
app.bin: m1.o m2.o m3.o
Good luck,