Ammonia smell in coop-first time owner

[beach chick]

we finished our 12' x 12' WIR in about October. come November, I ended up putting tarpaflex rather badly - in a severe gale with horizontal rain - on 2 sides, using cableties to attach to the wire, and I had to cut the sheet on the front to allow access to the door and pophole. I did try and anchor it down with bungees but not very successfully.

 

it has been pretty wet in there at times, so far I have just raked up the aubiose to try and shake it out a bit so it can dry (if/when it's ever not raining or freezing).

 

with all the snow, rain, wind, gales etc etc since then, the 2 sheets I have put up have ripped really badly, so I'm thinking come the better weather to start again. I'm planning to staple gun a permanent covering onto the door and pophole cover, but cant work out how to cope with the bits in between, which are really where the worst rips are - should I just leave these open and accept I cant fully waterproof the whole thing? - the pophole is open all day so they FR inside the electric fence.

[Plum]

I a piece on per panel on the cube and door side and over the cube OH made a small overhang of roofing so it doesn't need a tarpaflex. It just comes out about 18" and slopes away from the run. See if I can find a pic.

 

This one shows the small shelter