I actually had this same problem for a short time in college, and it was pretty easy to stop, so don't worry too much about it. That probably just makes it worse anyway. What you need to do is develop a little concentration. Breathe in and out through your nose and just learn to follow the breath. When you feel that urge to clear your throat, just do this breathing thing.
Your mind is probably jumping around, and your brain is just doing this throat clearing thing as a subconcious reflex. You can't ever get it completely "clear" like your mind wants, so you just have to teach your brain to be ok with the way it feels. If you can keep yourself from doing it for just a little while then it will get easier.
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"I was made to love magic, all its wonder to know, but you all lost that magic many many years ago."
N Drake