If you want to stay away from chemicals, this is the way to do it.
Fresh sprigs of Rosemary (about 4-6" long), spread around the perimeter of the run, hanging in the coop and right around the coop helps eliminate flies. We have a Rosemary bush, and whenever we trim it (just like other hedges), we spread the trimmings and it has worked great! There are other herbs that will help and I'll update this, as I find out more "helpful hints".
I combed through a lot of similar posts asking for help with flies. I don't know how to reference one post, to add this to all of the posts at once, that are asking this question, so will post this here, in hopes a moderator will see it and spread it where it needs to go, or combine all the posts of the same question, so it's easier to find. Please feel free to delete this, if I'm not supposed to put this here. Thank you.
Edited by Ellenaj - 5/5/16 at 1:11pm