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Beautiful! Such craftmanship!
Have wanted to make one of these for some time. Where did you get the metal (non-wood) parts? I'd like to hear more about them.
The prevention suggestions here are most appropriate, but they don't rid you of the present problem. Dribble a little dish soap (any kind) in your container before adding the apple vinegar. Fruit flies can land on the surface of liquid, but the soap breaks the adhesion characteristics of the liquid causing the flies to drown.