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IM messages seem to be documents just as much as email or many things you'd normally call documents. A reasonable definition IMO would be:

    A self-contained rich formatted text file/package that optionally contains attachments or media.
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I'd disagree with that for most messaging apps. If you think about Discord or Slack for example. You have a plain text message and then media attachments externally. This could be very well expressed with JSON.

Very few messaging apps let you go beyond plain text and let you start embedding media or complex layouts inside a message.

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Eh, XML is a machine-readable generic markup language. Why would you prefer using a less powerful format like markdown in a context like message representation? XML with inline tags seems the perfect fit.
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Less powerful also means less complex and less exploitable. You can very easily grab a markdown renderer rather than trying to decode a .docx for messages.

Pretty much no messaging apps let you create messages more complex than markdown anyway.

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