1. A method for compiling a high-level language (HLL) program, comprising: performing on a programmed processor operations including: inputting a command having a first field that indicates a set of one or more HLL source files to be compiled and a second field that indicates a set of one or more functions that are to be implemented on programmable circuitry of a programmable IC; for each HLL source file of the set: in response to the source file including one or more functions of the set: for each of the one of more functions of the set: generating a respective netlist from HLL code included in the function; generating interface code for communication with the netlist; and replacing HLL code of the function in the HLL source file with the generated interface code; compiling the HLL source file to produce a respective object file; and appending the netlist generated for one of the one or more functions of the set to the object file compiled from the HLL source file that includes the one of the one or more functions of the set; linking each of the object files to generate a program executable on a processor of the programmable IC; and generating a configuration data stream that implements each generated netlist on the programmable circuitry of the programmable IC.