Advice request - if anyone cares to opine I’d appreciate it:
Haul out and replace all the covered run floor litter material, or leave this and build it up even higher, to create a floor of litter - a forest floor essentially - deep enough and high enough to not get wet from below? Is that even possible to do, and is it safe for the chickens?
What’s in there now is wood (ramial) chips/ TSC large wood shavings, / collected leaves & twigs / chopped hemp / a little bit of rice hulls /whatnot added through the year.
Two corners of the covered run are getting consistently really wet. Only one corner is consistently dry. Partly due to the leaking roof I think, which I’m going to hopefully rectify (tarp underneath so that the leaks run off is DH-approved Plan A, Plan B is @bgmathteach’s idea to silicone seal all 240 screws, a difficult ladder-intensive but possibly effective solution).
I’m pretty sure a lot of the water is from the ground below not draining well. We’ve had a serious amount of rain here in the northeast exacerbating this situation. In winter any surface water flows on top of the frozen ground too. Today after a rainy spell I saw standing water just outside the run near one of the corners.
Last winter whenever the snow melted some, I would sometimes see the litter getting damp, and digging down some I could see water. I’d add more stuff on top to keep everyone dry, also because when it got cold again the wet stuff would freeze up hard.
My usual plan every year has been to hoe out the litter in the Fall, and replace a lot of it and add as the year goes on. It does make great mulch.
This summer one corner has been sprouting mushrooms, I think the ramial chips I used are old and perfect mushroom material, and this concerns me so I’ve been raking them out when I spot them. I don’t want to be growing mold! Basically the litter is composting before my eyes. This is what a forest floor does. Could I or should I build or not build on this?
Seems to me also it’s a good idea to not have chickens potentially scratching around in years and years of accumulated poop that for a large part of the run can’t really wash away and be exposed to good sunlight? Would poop-borne diseases be concentrating? This run goes from nice dry spots to the wet composted spots.
I have no problem with the time & labor of hoeing it out and putting the great mulch on the gardens and blueberries. I recall this is what 
@rural mouse did this year. It’s a big job but do-able over a few days, did it last year and the year before. I also can buy or haul as much replacement litter I need to make a pretty deep litter floor. I will look for newer ramial chips if I use them (more than a year old but not growing weeds already).
What would you all do?