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As for Japanese settlements in general, there were:
- villages, towns built around castles, fortified samurai residencies, these types came into fashion after the rise of the samurai class
- planned towns, cities, these are obviously the work of centralized governments, be it imperial or local
- post towns/villages, these were set up along existing roads, where they offered various services, inns, rest-houses, clothing, etc.
- farming villages, these were situated at open fields, they bunched up the houses at a place they regarded as the least suitable for rice fields (or orchards), and they cultivated as much land around as they could
- fishing villages built near the coast ofc!, how they were built really depends on the specific location, I started to gather screenshots from google maps of various types