Communications infrastructure for modular reconfiguration of FPGAs needs to support the changing communications interfaces of a sequence of modules. In order to avoid the overheads incurred by a bus system or network-on-chip, the approach we have taken is to create point-to-point wiring harnesses to support the dynamic intermodule communications. These harnesses are reconfigured at various stages in the application as necessary. The COMMA methodology implements applications on tilereconfigurable FPGAs such as the Virtex-4. This paper outlines the methodology and describes greedy and dynamic programming-based algorithms for merging configurations, which is a central process in generating wiring harnesses within the methodology. The effects of merging the configuration graphs were explored with both algorithms for a range of device sizes and architectural parameters. Our evaluation indicates graph merging using the greedy method can reduce reconfiguration delay by up to 60% and the dyna...