No, no...
This is easy to fix. If you are going to use pine shaving you have to keep the area relatively dry. A covered / roofed coop/run that has good drainage around it so no heavy water comes in. If that is not possible switch to wood chips.
Now for flies, Two little things keeps them in check for weeks at a time. Sweet PDZ and martins permethrin 13.3. Don't get powder, premixed fly spray, permethrin 10...
Get the 13.3 and mix it for fly control. Mixing directions comes with the bottle for animals, building foundations, bugs.
Clean the coop/run changing out shavings. Sprinkle a little PDZ around. put down new pine shaving. spray everything with a bug sprayer mixed with 13.3 permethrin @ about 1 1/2 oz per gallon.(read directions). spray 6' to 10' around the perimeter of the coop run.
You will have to spray again every two or three weeks but no more flies EVER! If your pine shaving are wet for more than two day, rake them out and go again. I have been doing this for going on 4 years and know this all to well. My roofed coop/run and nest boxes are pine shavings with poop board and outside run wood chips.
No flies, no smell if i follow simple rules.
1) good drainage
2) keep inside dry and change pine shavings when wet or every two months.
3) Keep adding wood chips outside as needed.