How difficult is it to modify this to work with top-down level creation instead of sideview platformer? Does this have the latest version of the auto tile extension?
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As for autotile but for top-down, all you need is your top-down tileset, but it must follow the same rules for the Autotile extension tileset (can be found on the extension itch page), the system in the template should be the same.
No, the template have the older version of the extension, you can get the extension latest version from its itch page, and you can import it into the template without any problem, the latest update for the extension does not break anything.