Dancing Hoskuld
Deity
Here are the buildings that requires a stone deposit somewhere around a city:
BUILDINGCLASS_STONE_QUARRY
BUILDINGCLASS_JAPANESE_SHALE_PLANT
BUILDINGCLASS_SANDPIT_STONE
BUILDINGCLASS_BORAX_MINE
BUILDINGCLASS_CHALK_PIT
BUILDINGCLASS_COBALT_MINE
BUILDINGCLASS_FOSSIL_NEANDERTHAL
BUILDINGCLASS_FLUORITE_MINE
BUILDINGCLASS_GRAPHITE_MINE
BUILDINGCLASS_QUARTZ_MINE
None of these seems to me as a local expansion to an already established large scale stone excavation in the area.
To me the logic here is, if the city has a large high quality stone deposit close by, then it may also have enough borax, chalk, shale, quartz, cobalt, fluorite and graphite deposits to warrant the construction of these other types of mines in the area.
This is done to allow more resources without having more on the map. There are quite a few of these for the different mine and quarry map bonuses. It is just a way to add a bit more flavor and difference while getting a bit closer to reality. The Rio Tinto region in Spain provides many metals but even in the biggest maps would only take up one plot on a Civ IV map. Do we have it just provide one metal of add some other seemingly unconnected local requirements to give something that resembles reality?
I see no logic at all for why the Pigeon Coop and Lizard Catcher would require a stone deposit close by to warrant their existence.
These were from before we had those animals in game. Easy enough to change them to animal buildings.