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Assuming this happens with the front brake, cause that's the one you use the most.
Try getting on the bike and standing it up with the engine off.
Hold the brake lever on and try rocking the bike back and forth.
If you can make it clunk that way it might be easier to tell where its coming from.
Odds are that its just a loose brake caliper or steering head bearing.
If you can't duplicate it that way, just go over every bolt in the front end, including the rotor mounting bolts to make sure nothing is coming loose on you.
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