FPGA-based Configurable Computing Machines (CCMs) offer powerful and flexible general-purpose computing platforms. However, development for FPGA-based designs using modern CAD tools is geared mainly toward an ASIC-like process. This is inadequate for the needs of CCM application development. This paper discusses an application framework for developing CCM-based applications beyond just the hardware configuration. This framework leverages the advantages of CCMs (availability, programmability, visibility, and controllability) to help create CCM-based applications throughout the entire development process (i.e. design, debug, and deploy). The framework itself is deployed with the final application, thus permitting dynamic circuit configurations that include data folding optimizations based on user input. The resulting system aids in creating applications that are potentially more intuitive, easier to develop, and better performing. An example application demonstrates the use of the application framework and the potential benefits.