My reaction to the phrase "clay and stone and freshly shattered flint" is that he means that whatever material was blown up by the shell included these materials.
Flint is a kind of stone. The word "stone" by iself suggests the kind of tough material that is strong, does not break easily, and breaks into compact lumps. Flint shatters easily and produces sharp, flat shards. Prehistoric man produced sharp-edged tools and arrows by chipping flint. He's saying something about the composition and the texture of the material produced by the explosion.
Because flint is very hard and sharp-edged, when it is struck against steel it breaks off tiny fragments. The fragments are so tiny that they spontaneously combust and produce white-hot sparks. Thus it is a traditional way of making fire (and was used in early firearms, "flintlock" guns). But I don't think that's what he means.