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Currently for .md(x) files the following regex is used: /\[.*?\]\((?:<((?:\(.*?\)|.)*?)>|((?:\(.*?\)|.)*?))(?: ["'].*?["'])?\)/gm. This targets [link text](/url/or/path) style links.
Instead of complicating the regex to also match ref. links it's probably easier to do another regex match pass for something like /\[.*?\]\:\s*\n?\s*(URL_REGEX_HERE)/gm. That should match [link id]: /url/path style links.
BTW I'd extract the URL_REGEX in both cases for readability.
E.g.
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