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At the heart of Starbound's colony building system are Tenants. These are spawned in by placing Colony Deeds in enclosed structures, with each one preferably contain one #door and one #light tag each (there are some unique exceptions).
.tenant files control the sort of Tenants that spawn and govern mainly what tags are required, and what the Tenant will provide in rent.
Even though your .tenant files may pass a JSON parser, if the game does not agree with the coding, it can cause your players to not spawn Tenants. For instance, using brackets where there normally are none may result in this issue. It will not crash your game like the .npctenant file, but it can be pesky.