The Deep Litter Method??

[BFG Central]

Well you keep the eggs clean by changing bedding in the laying boxes once a week.
It may need doing more often if you have a lot of rain but even then you can guard against this with gravel on the ground and a tarp over the first 3-4 ft of the run from the chicken coop.
That way the chickens feet stay mud free.
Iv spoken to a friend that keeps chickens commercially and its common practice to leave the mess down and cover over with sawdust.

Its true that my chickens get cleaned out when it starts to look really messy and not before.
The wood floor is covered with vinyl flooring which is great for when your cleaning out. It also means it can be hosed out and disinfected and the wood does not rot or have anything nasty lurking in the cracks.