In the Cyclone III device handbook, Volume 1, Section II, Chapter 7, Table 7-5 says, "The PCI-clamp diode needs to be enabled for 3.3-V/3.0-V LVTTL/LVCMOS." Table 7-8 says, "The PCI clamping diode must be enabled for input signals at 3.0 V or 3.3V."
If you do not have the built-in clamping diodes enabled, you have to provide them externally. There might be pins that don't have an internal diode available and so always require an external diode for these I/O standards.
I haven't looked at the app note, but the handbook also says this on page 7-14:
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For more information about Cyclone III PCI-clamp diode support, refer to AN 447: Interfacing Cyclone III Devices with 3.3/3.0/2.5-V LVTTL/LVCMOS I/O Systems.
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