How to create a simple Cpu??

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Qsys is a system generator. So you need existing modules and Qsys connects them together. The NIOS is an existing processor. If your job is to create a processor in VHDL, you probably dont want to use Qsys. He possibly has a VHDL file and a .bdf (graphical schematic) file.

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You are right, does this mean i have to write the vhdl code for this processor from scratch. Oops this is not going to be easy