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I dont know how or why this Mapshots folder appear, but i know that it will always appear even if the project dont use the plugin. I think that the deployment process copy everything on Steam\steamapps\common\RPG Maker MV\nwjs-win to the deployed project, and the Mapshots folder is there. About the default assets I dont know. When I delete then they dont go to the deployed project, maybe in your case the img folder is in that nwjs-win that i told before. But i really dont understand how the process works and dont want to broke it, soh i leave that folder untouched