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40d:Refuse stockpile
Your dwarves will bring mostly animal items to a refuse stockpile, such as chunks, remains, bones, shells, skulls, corpses, raw hides and any rotten items. This helps in avoiding miasma from rotting items in your fortress, if the stockpile is placed right.
It is useful to keep a refuse stockpile outside, where no miasma is created, and/or in an enclosed room next to your butcher's shop to store corpses waiting to be slaughtered, prevent clutter, and lock in miasma from rotting butcher leftovers. Butcher's shops tend to become cluttered very quickly, as a single animal already "bursts" into many items.
It is also useful to keep a refuse stockpile holding only shells, skulls and bones near your craftsdwarf's shop for bone carving and bowyer's shop for making bone crossbows. Such a stockpile will not create miasma because nothing in it can rot.
You can provide your stockpile with 2 doors arranged as an airlock. This will mostly prevent miasma from spreading when a dwarf steps through. You can contain miasma completely by building a diagonal entrance to the refuse area, since miasma cannot travel diagonally. v0.28.181.40d
Details
Corpses, chunks, body parts, skin, and food all can rot, emitting miasma when stored on Inside Dark Subterranean tiles. It is important to know where you want to place your refuse stockpile beforehand, as miasma causes an unhappy thought. Designating a refuse stockpile on any tile with Light Above Ground will prevent miasma and makes the items subject to occasional (when exactly?) cleanups (this includes bones, skulls, and shells!).
Alternatively, you can dig an open pit down to the z-level most convenient for you. Light need only touch the tile once for it to become permanently Light Above Ground, after which you can rebuild the roof.