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Project templates should go into ezpublish/Resources/views.
They can then be referenced in code without any prefix: ezpublish/Resources/views/content/full.html.twig can be referenced in twig templates or PHP as content/full.html.twig.
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Project assets should go into the web folder, and can be referenced as relative to the root: web/js/script.js can be referenced as js/script.js from templates.
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The recommended method is to version the whole ezplatform meta repository. Per installation configuration should use parameters.yml.