I spoke to a colleague, a geneticist who raises fruit flies, and asked him how to eliminate them. He can't use chemicals - they would kill his stocks, so he is in the same boat as bird keepers. He has a cheap and simple method that he swears by. Get a soda bottle (empty) and put some banana peels in the bottom (fruit flies love these). Get a short stemmed funnel and place it in the mouth of the bottle, stem down. The flies will fly down the funnel into the bottle, but they will not be able to find their way out. No chemicals, just bottles of fruit flies. Works for him.