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Similar to customizing individual parts of the rendering, you can have different themes that can be shared.
Now create a new directory for your theme at
/path/to/custom/templates/my_theme/html. Create a file
layout.html.twig and you can customize the layout that wraps all generated html files.
Even with a theme, the rendering engine will continue to
default directory (e.g.
as a fallback for any templates (see Customizing Rendering).