Remove the food source. Think maggots.

The flies are breeding somewhere and something is attracting them to your home. They love the aroma of putrefaction and can detect just a few molecules per liter of air. That aroma can be disguised from the human nose with various canisters of floral scents. But a fly is okay with the thought of fruit piled on top of something rotting. In fact, fruity rot is a good thing. If you're a fly.

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