To use SPI pins as general-purpose I/O (GPIO), disable the port option for both "Slave SPI Port" and "Master SPI Port" on the Global Preferences tab in the Spreadsheet View tool of Diamond.
To use the CDONE pin as GPIO, set CDONE PORT as "CDONE_PORT = CDONE_USER_IO" on the Global Preferences tab in the Spreadsheet View tool of Diamond.
Refer to FPGA-TN-02014, CrossLink Programming and Configuration Usage Guide for more details.