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I managed to get a simple programm (something like Hello World) to be compiled directly from the eclipse workspace.
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That would be only possible if you manage to make Eclipse use a make file, linker script etc., that is done according to the rules the NIOS-Linux build system enforce. See the make files for user land programs generated by enabling them in "make menuconfig" within the build system.
I suggest to first create a hello world example by doing a new directory under "vendors" (as suggsted in one of the links) and adding same to the main build script. This is the correct way to do your own userspace programs (and drivers). Then you might try to make Eclipse use the appropriate scrips to compile (and debug) your C code.
-Michael