1. A self-modifying FPGA system, comprising: an FPGA; a configuration memory coupled to the FPGA for providing the FPGA with configuration data including SAFE configuration data and dormant configuration data, the configuration memory including a PROM and SRAM; wherein the SAFE configuration data is initially loaded to the FPGA and the FPGA is configured to a safe operating mode, and upon a determination to proceed to a next step of self modification, dormant configuration data contained in the configuration memory is loaded into the FPGA and the FPGA is configured to a secure operating mode; and wherein the SAFE configuration data includes user mode logic functionality to read data from the PROM and write data to the SRAM appropriately to transfer dormant configuration data contained within the PROM to the SRAM.