In the recent months, I've seen that many friends (many of them coders) started writing, long, elaborate mails with footnotes for link, meaning that they write paragraphs [1] and then [2] put the links at the bottom [3]. Like this.
[1] www.example.com/1
[2] www.example.com/2
[3] www.example.com/3
I think it is smart and everything, but I don't understand the process of putting the numbers while you write: I put the reference both when I write and when I edit the text, I swap paragraphs, thus I make a mess with numbers.
Is it a common practice used by some community or is there some editor/plugin that automatically puts the right number in footnotes? Is this mutated from Markdown?
definitely is not Markdown, that compile in HTML, so you should see an anchor instead of plain text.
I think could be an habit from people that want to send plain text mail (not HTML encoded) without use URL inside paragraph to keep readability. Maybe influenced by Markdown emerging community, where square brackets are used for footnotes. Instead of wiki-markup or LaTeX that use curly brackets for footnotes.
For a quick example, check the very own StackOverflow flavored markdown for links.
Maybe you should also check W3C Web Annotation Working Group for some news.