The Qsys migration guide says I have to add the QIP file generated by Qsys to the Quartus project. When I do this, quartus errors saying the Nios system instance is ambiguous because there is nios_system.v file in both the db folder and the nois_system folder generated by Qsys. This is true but why is there any confusion??? Quartus copied the file to the db folder itself. I started from a completely clean project folder with no db folder nor nois_system folder. Qsys generated the nios_system folder and the associated QIP file and Quartus generated the db folder with the nios_system.v file in it. What is wrong with these tools???