IIRC (not near my linux box right now), the "arduino" command is actually a shell script (bash, iirc) that sets up some variables, then invokes the java runtime to kick off the IDE. You would have to modify this script to pick up the command line variables and then pass them on as parameters to the java invocation. That of course assumes that they are then passed thru and interpreted by the IDE, of course (which I don't know off hand). If they aren't, then you have some java coding to do...