agricultural lime in powder form can be used to clean with. Remove the birds and dust everything. Let it settle for an hour or so, then you are good to go. Another way is the mix it with a little water to make a thick paint then paint it on... we rednecks call it whitewash. You can mix in a little diatomaceous earth into the 'paint' for some organic bug killer.
As with anything, use in moderation. Keep your birds out of the coop while you apply the ag lime and you should be ok.
People sometimes lime the coop or run for all different reasons. Disinfection (insofar as you *can* disinfect dirt, that is); odor control; reduce acidity of soil; reduce acidity of material in coop or run that you will later rake out and put in compost or on garden; etc. Different types of lime are more or less appropriate for different purposes.
That said, I don't use lime in my runs or coop, you certainly do not routinely need it.