I used sheet vinyl flooring and I like it. It is really inexpensive, easy to install, and a breeze to clean. I used a thick bead of silicone caulk around the edges to seal them. After installing the flooring with vinyl flooring mastic, I did leave the coop wide open for a week to off-gas before adding chicks. I use about 1.5" of fine pine shavings on top and 3 week old chicks had no difficulty. I think the regular flake style shavings would have been harder for babies.
It is not difficult to tear through the vinyl layer to the porous backing if you use sharp implements to clean it or drag objects with sharp edges. If this happens, the only option is to replace the floor as the tears will absorb moisture and odors. The whole back of my coop opens and I use a kid-sized plastic snow shovel to remove the shavings. Rarely are droppings left on the floor. I do wash the coop down with vinegar and hose it out every few months to deep clean.
