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It's absurd that quartus would do such a thing, since there is lots of hardware connected to these pins that could potentially be destroyed by this. Is there a way to prevent this, besides manually assigning every single pin?
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It's not
aburd. It's the way, Quartus and design compilers from other vendors usually hande unassigned pins.
Apparently, you are new to basic concepts of these design tools. Basically, the problem is created by defining I/O pins in your top design, that are not intended to be connected externally. Simply, you shouldn't do that.
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