Constraining Nios Design

I would first start with contraining your I/O. All the other violations could be coming as a result of your I/O not being constrained. Whether you can cut those I/O depends on what they are. As a general rule of thumb if your I/O will operate under any skew/delay then typically you can cut them, otherwise you'll need to constrain them. So if it was say a PIO connecting to a push button or LED then that would be safe to cut, if it was a high speed interface then you *must* constrain it.