Some pins of Arria V FPGA pins are multi-functional. For eg, Pin A6 has functions like IO/CLK13p/DIFFIO_RX_T3p/DQ1T. Termination guideline is provided for each function as below in Pin connection guidelines document:
CLK13p: When you do not use these pins, Intel recommends tying them to GND or leaving them unconnected. If unconnected, use the Quartus II software programmable options to internally bias these pins.
DIFFIO_RX_T3p: Connect unused pins as defined in the Quartus II software.
DQ1T: Connect unused pins as defined in the Quartus II software.
CLK13p says, if not used leave them unconnected or configure in Quartus II software. But the other functions says configure in Quartus II software. Whether I have connect to GND or configure in Quartus II softwate for these types of pins?
For unused pin, even on pin which can be used as user I/O pin when device is boot up, it is by default set to "as input tri-stated with weak pull up" by quartus.
You may leave it unconnected if pin connection guidelines states that "if not used leave them unconnected or configure in Quartus II software.".