Long-term solution is to provide more litter in the run. Right now it looks like bare dirt with the straw you just threw over the puddle. Bare dirt is bound to turn into mud and puddle when it rains, or when snow melts. Get a large load of wood chips in that run, and mix them in with organic matter as the seasons go by - grass clippings in the summer, leaves in the fall, whatever other yard waste you can find. The more plant matter, the better. And lots of wood chips. That will improve the drainage and will stop mud from forming. Bonus#1: it will turn into a nice compost. Bonus #2: it will be more fun for the chickens. That's what I have in my run - it gets snowed on and rained on but doesn't get muddy and there are no puddles.
This is what it looks like after a day-long rain:
This is what it looks like after a day-long rain:
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