It would be best if I could actually pass single lines of raw code to the Arduino for it to then execute. Example: I would enter "digitalWrite(13, HIGH)"
However you do the comms, (USB or xportm etc) the AVR will be getting the commands through the serial port. You wold set up the serial port appropriately, and use Serial.read to grab a byte/char at a time.
As for send lines of raw code for the AVR to execute, this isn't possible. The C code is compiled before being loaded to to the AVR.
However you acn always write a parser to interpret the commands you send and act on them accordingly. If it were me I would shorten what you send from "digitalWrite(13, HIGH)" to something like "dw13h" or "dw13l". It would still be human readable and easy to parse by your program.
Mike