I free range so that they have fresh soils under their feet all day and aren't living on and eating the soils of runs that are contaminated with high loads of feces. If you cannot free range, paddocks that are movable are an option. If those are not an option, doing deep litter in the run and using it for composting the feces and improving the soils can help.
I utilize deep litter in the coop so that the soils there are not overloaded with fecal matter also. The litter bonds with the feces and composts in place, where beneficial bacteria, bugs and worms can change poop into soil. Good ventilation keeps the ammonia smells down, flies are not attracted to the feces and the litter insulates the coop floor in the winter, as well as providing the birds a place to scratch, dust and congregate on snowy days.
I usually don't feed on the ground...no need to put their food where they poop, so all feed is dispensed in a feeder except for the occasional food scraps or training grains.
I cull each year in March for those who are not laying every day or every other day. This seems, by sheer probability, to also eliminate the birds prone to parasites, illness or laying issues, as I never have any issues with these problems.
I let the birds forage most of their dietary needs and only supplement a little in the evenings and then feed regular rations in the winter. The superior foraged nutrition is more adapted to their dietary needs than is grain based feeds and the exercise is important to their overall health.
I add things to their diet~ on occasion~ that are known antihelmintics such as pumpkin seeds, garlic, ginger root, etc. just to see if anything comes out...never have seen a worm in the stool, so I'm thinking we are good.
I feed fermented feed so that their bowels are healthier and less prone to harbor heavy parasite loads. Before the FF I always kept mother vinegar in their water for the same reasons. The fermented feed helps guard against cocci, salmonella, e.coli and other harmful pathogens, as well as increase nutritive values of the feed.
Mostly I just watch for general health, appearances and production levels and if these all are optimal, then I know the parasite load they are carrying is an acceptable load and so I don't worry about it.
They say that 90% of a flock or herd's parasite load is carried by 5% of the group, so I'm thinking I am probably eliminating that 5% by doing yearly culls of non-thrifty animals, those not laying, etc. By eliminating these animals that are more susceptible, I also eliminate those that are shedding oocysts into the soils so that the other birds may consume the insects and worms that have feasted upon them.
A few all natural antihelmintics are the pumpkin seeds, garlic, castor oil, ginger beer or ginger root, black walnut hulls, soap of any kind, but they sell a concentrated soap called Basic H that is all natural (Joel Salatin uses it on his livestock).
My granny always fed her chickens and pigs her soapy dishwater~she used lye soap~because she said it was good for their health..and she was right, it acted as a dewormer. Soap is a surfactant and can dissolve the protective oils on parasites skin and eggs, making them vulnerable to digestive acids.
Another preventative measure is to buy stock that is known for natural hardiness...starting out right can make all the difference in the world. I choose breeds based on that and I cull for that in my flocks, so I seem to get unnatural long laying life from the breeds I have.
I think a combination of these methods yields the healthiest flock one could ever have...I've never had illness in my flocks and that has to mean something other than sheer luck~to me it's the culmination of the efforts described above that insure success.