1. A method for creating a mask-programmed configurable integrated circuit that includes a reprogrammable structure, comprising: (a) receiving a description of circuit functionality specified by a user for implementation with the mask-programmed integrated circuit, the description of circuit functionality including a description of non-reprogrammable functionality and descriptions of a plurality of programmable functionalities to be selectively and alternatively implemented in the reprogrammable structure of the mask-programmed integrated circuit; (b) automatically modeling the reprogrammable structure to be capable of alternatively implementing each of the programmable functionalities; (c) performing physical layout for the entire mask-programmed integrated circuit, including the reprogrammable structure as well as circuitry to accommodate the non-reprogrammable functionality.