I think there may be a misunderstanding regarding the mapping between plug-ins and project types. The Microtronix project types that you see (kernel, filesystem, and application) do have a corresponding plug-in but that isn't always the case.
The linux.gtk plugin is probably the SWT GTK translation code. It has nothing to do with Nios II Linux.
Developing uClinux apps is described within the Reference manual that comes with the Nios II Linux distribution. At least the basics are described there.
I hope this helps... Let me know if I've confused you even further.
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