FreeOrion

Currently the roles of Buildings and Specials overlap somewhat. While generally you find a special on a planet, and construct any buildings, specials can be built (i.e. the Gaian). The other distinction that i'm aware of is that IIRC, specials can operate on non-imperials inhabitants, while a building does nothing for minor species.

Perhaps we can think of them this way: Specials are intrinsic to the planet, and remain unless the planet is utterly destroyed, while buildings are subject to destruction via bombardment.

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As far as I know, a building should work on any object that meets its effectsgroups' scope conditions while its activation condition is met. Being player or non-player owned shouldn't matter.
Special can be applied to any object, not just planets; buildings could have a special attached, for example, or systems or ships or fleets. But yes, in practice, specials just add some effects groups to the object they're attached to. They could also be checked for by conditions, to affect scope / activation of other effects, though I don't think that's done much yet.
Sounds like you might want to add a structure meter to buildings, to track their progress toward destruction?

Well, i do want things to blow up when we add bombardment.
But rather than adding more stats to the game i'd probably lean toward having a semi-random chance of individual buildings being fully destroyed based on the PP that it took to make them, and the strength of the bombardment.

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I was thinking more along the lines of being able to target particular buildings with bombardment or invasion... After all, buildings are rare compared to other games, so we can afford a bit more depth/complexity to them.

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I think disabling or destroying single buildings is something better suited to spies than to ships. If only for interface reasons, dealing with a very limited number of spies with a more detailed system of targeting buildings seems more practical than dealing with potentially many more planets and ships requiring a detailed targeting system to be fit into their existing UI mechanisms. This would also give spies an important role that is distinct from ships and invasion troops.