HTML comment tags break Markdown list indentation

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Markdown has no notion of comments and it supports HTML in a very limited and restricted way. What you describe as “obviously wrong” is would only be obviously wrong if the Markdown were embedded within HTML – i.e. if HTML was the primary syntax and Markdown was the secondary/foreign/embedded syntax.

But for Markdown and the CommonMark spec, that is not the case. It is the HTML that is embedded within the Markdown, it is the HTML that is foreign and secondary. Neither Markdown or CommonMark are trying to reimplement HTML, nor would it be a good idea.

Per the spec, HTML blocks are treated like any other block level element, including that they will interrupt lists, just as a block quote with the same indentation will.

If you still think this is a bug, you should post it as an Issue against the CommonMark spec.