I seen on a level once, it wasn't quite an upgrade system or a plugin system, but once you built the phychic beacon (I dont think it was this building but it will do for an example), it would dissapear from the sidebar and then enable the paris tower (in the sidebar). I dunno if thats relevent to this but i thaught i could send you the level and see what you think. e.g you build a tesla command center, then you get the ability to build the adv. tesla command center but lose the ability to built the tesla command center.
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