The tedious method, bagging the fruit with mesh bags? I cannot think of another way to do it. As you say, sprays are a no no. Better ventilation, to disperse the smell of the ripening fruit, (but that might spread the smell to a wider audience!). What about traps, with a sugary fruit syrup, plus soap? The combination attracts, then kills! It works for low numbers, but swarms might be a challenge. Worthy

Flies!? Yyeecchh! And I thought skeletonizers and mildew was bad enough! It might help to make the flypaper renewable: to get true flies, use brown waterproof cards coated with petroleum jelly. On a regular basis, scrape off the petroleum jelly and dead flies, and apply new jelly. Fruit flies, whiteflies, greenfly, blackfly, and leafhoppers respond better to bright yellow cards.