Why are there Prohibit constraints in the UCF file? Can they be removed?
Most of the prohibited pins are pins that are also used for configuration.
These pins are prohibited, to call attention to the user that these are configuration pins. If the user is aware that these pins are also used for configuration, they can also be used as normal IO pins.
However, PCI signals should NOT be placed on these pins.
Other prohibited pins that are not dual purpose configuration pins are prohibited so that customers can migrate between different core versions and maintain a consistent pinout. For example, users of the 66 MHz PCI Core which requires a regional clock will find that the PCI pinout also prohibits a global clock pin. This is so that if the customer chooses to migrate to PCI-X which requires a global clock that pin will be free.
If migrating designs and pin consistency are not concerns, these prohibited pins can be used for other reasons.