There is a folder corresponding to each Zone ID. Within those folders are files that apply to only that zone. If a file does not exist, that zone has no data for that particular feature.
The following files, if present in the folder, may be loaded:
Script.txt - Instance script (triggered spawns, teleports, etc).
EssenceShop.txt - Holds contents of essence chests (any chest that exchanges essences/tokens/keys/etc for items).
Shop.txt - Holds contents of NPC vendor shops.
Static.txt - Holds a list of static NPC objects that are spawned globally (not by spawn points).