OK guys...tell me, what am I missing here???
I just have my plywood subfloor, and then lots of litter (straw and shavings) on top of that. It would be virtually impossible for a hen to drop a turd and hit the plywood below. Instead, all droopings land on the litter, where they dry out. I go in their every couple of days and stir things up. With deep litter (or my semi-deep litter method), the floor stays dry. Over where I have the feeder and waterer, I have an extra scrap of plywood under those, in case I spill water. So...all of that having been said, why use a pond liner, canvas, linoleum, etc? What am I missing? Clean up is still a matter of raking, shoveling, or sweeping, so I don't really see the need for some waterproof substrate.
This is a little like the decision whether or not to use the arm rest protectors that come with your new sofa. Some people use them right away, hoping to preserve their new sofa and waiting until the covers get dirty before they take them off. Others wait until the arm rests begin to show some wear, then put on the arm rests that they have saved to use (to cover up the dirty sofa arms).