I have a little courtyard - and a million flies - how do I get rid of them!!?

I am growing basil, thyme, chillie, coriander, chives, mint, parsley, rosemary and cherry tomatoes in a few pots in my little courtyard and I have noticed an incredible amount of flies lately - they are ONLY in my courtyard and not hanging around the front yard etc. What the heck do I do to get rid of them? I bought a fly-trap to get rid of them but because of the fly "attraction," (the smell to lure them to be caught) - my 4mx4m backyard now also stinks! I can’t even have drinks outside because the flies go into my guests wines! I've never seen so many flies since being near a horse stable! What do I do??? With the amount of flies I have, you would think that my gr was green manure!