Personally; I make all ports between switches trunks. If you have a network core feeding multiple buildings each with its own set of VLANs, on the network core I would configure the allowed VLANs, so traffic from a VLAN in one building can not end up in another building where it is not needed. Typically - I would only do layer 3 routing at the network core, rather than in buildings downstream - to keep things simple and easy to maintain - but I guess if the buildings were really big I would consider doing L3 in each building itself.
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