Specific hardware customization for scientific applications has shown a big potential to address the current holy grail in computer architecture: reducing power consumption while increasing performance. In particular, the automatic generation of domain-specific accelerators for General- Purpose Processors (GPPs) is an active field of research to the point that different leading hardware design companies (e.g. Intel, ARM) are announcing commercial platforms that integrate GPPs and FPGAs. In this paper we present a new framework with a holistic approach that addresses the challenge of design exploration of specific application accelerators. Our work focuses on a target platform consisting of a GPP with a reconfigurable functional unit. The framework includes a reconfigurable 1-core 1-thread OpenSPARC with a new programmable specific purpose unit (SPU) inside the OpenSPARC core. In order to program the SPU we have developed an automatic toolchain that profiles an application and discovers its main computing bottlenecks. With that information our toolchain is able to both design hardware specific accelerators that can be automatically mapped in the aforementioned SPU, and generate the binary code necessary to run the application using those accelerators. The OpenSPARC with the new specific application accelerators, defined in a Hardware Description Language, can then be executed and measured. Still awaiting further development, nowadays our framework is a proof-of-concept that shows that this kind of systems can be developed and programmed as easily as a GPP. In a near future it would be the source of very interesting information about the capabilities and drawbacks of those mixed GPP-FPGA systems.