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Has the "Unused Pins" setting default been changed yet? If not, that would have to make your list. I once spent an entire day trying to figure out why my simple LED-flasher design wouldn't run on a Nios development kit. Turns out that the project had defaulted to setting all unused pins to "As Output Driving Ground."
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I agree this "burns" a lot of us. Pun intended. The reasoning behind defaulting as outputs driving GND is for power consumption reasons. Floating inputs may oscillate with noise causing unwanted power consumption. For a large device and package this really adds up. The downside is when using dev kits and not remembering that this setting must be changed every time!
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