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This chapter dissapeared in the CIII device handbook (why?)
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I guess, the authors finally realized, that it isn't actually safe operation to require the external 5V level to vanish during configuration ... This has been true for previous devices as well, but since Cyclone III, every third handbook page (or so) has a warning
keep the Cyclone III voltage limits.
In my opinion, the PCI clamp diodes shouldn't be used for 5V input unless the 5V source is automatically disabled for an unfigured FPGA. Otherwise 74LVC, external schottky diodes or resistive dividers should be used.