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This hardcoding is only necessary if you have a board that has an external configuration system supporting the reconfiguration request pin. Typically the board has a pullup on the signal so if your design doesn't drive the pin then the pullup will make sure the external hardware doesn't attempt to reconfigure the device. Often designs that don't drive this signal out reserve all unusued pins as input tristate which has the same effect.
The only reason why I brought up this pin is because when this thread started Quartus used to tie unused I/O to ground by default which would cause this reconfiguration cycle to constantly occur if your user design didn't contain that pin. So if your user design doesn't have that pin and you are running into this issue it might be just a matter of going into the device and pin options and changing the unused I/O setting from ground to input tri-state.
Note this isn't a Nios II or Qsys thing it has to do with the board being driven a signal and the possibility of Quartus pulling that signal low if you don't have it in your design.
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Perfect.
Thank you again!