Honored Contributor
Honored Contributorhi... you can modify the code directly in the plugin and when you re-build your kernel project, the changes will be reflected in your new code.
As a side-note: A bug in the current release of Nios II Linux currently rebuilds the entire kernel project each time since the nios2_system.h file is constantly being rebuilt. I would recommend setting the <kernel_project>/build/include/nios2_system.h file to read-only unless you're constantly changing your target hardware... it's a kludge until our maintenance release is out but it should help.
