fx3: Perform "warm" GPIO reconfiguration when enabling flash access

This fixes issue #196.

A "warm" IO reconfiguration is required, otherwise the FPGA's nConfig
will be reset to a default of CyFalse (resetting the FPGA).

Additionally, the firmware.c and associated functions have been renamed;
these are flash-related functions in general -- the "Firmware" name was
misleading.