Should be easy to add command line arguments for in and out. (I wouldn't personally advocate a configuration file.)

Don't be put off by run65816 being a wrapper for lib65816. It's a consequence of Sam writing a separate library, which is a good thing - it allows emulation of different systems without any need to adapt the original. It's a much easier way to work with than wrestling with something monolithic. lib6502 and run6502 are arranged the same way.