Disk Brake shudder felt through fork and frame
First thing, assess your headset. A loose headset allows feeble vibrations to make the bike shudder. This  tutorial over at Art's Cyclery will guide you through the process of taking care of it: all you'll need is a medium sized Allen Key.

If the headset looks just fine, it's time you get to your break calliper and rotor. I recommend that you sand your rotor and break pads a bit (until they look nice and smooth) with a medium grit sandpaper, wipe them down with some 90% v/v isopropyl alcohol nicely, reconfigure and bed them in. Also make sure that the calliper is aligned just right, if the calliper isn't approximately parallel to the rotor, it can make the thing happen. I would recommend using the business card method to align the calliper. Doing this will almost certainly cure the bike of the issue. 
I hope this helps. :)

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Edit: Also make sure that your pads have enough braking material on them before reconfiguring them.