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You can disable Markdown’s indented code blocks in Eleventy. Read more: 11ty.dev/docs/languages/markdown/#there-are-extra-and-in-my-output @LeaVerou/1468217083192352773
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(for the record, I do want to explicitly state that this also allows you to keep using the triple backtick for <pre>)
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Do note that starting in Eleventy 2.0 this feature will be disabled by default. Instructions for re-enabling in 2.0 can be found here: 11ty.dev/docs/languages/markdown/#indented-code-blocks