Alternate script to convert MultiMarkdown inline links to references (based on script by Brett Terpstra -- http://brettterpstra.com/project/markdown-service-tools/) Uses the link text instead of the URLs to create the reference names.

gistfile1.txt

#!/usr/bin/env ruby

def e_sh(str)
    str.to_s.gsub(/(?=[^a-zA-Z0-9_.\/\-\x7F-\xFF\n])/n, '\\').gsub(/\n/, "'\n'").sub(/^$/, "''")
end

def mmd_linkname(str)
    str.gsub(/[^a-zA-Z0-9]/n, '')
end

def find_headers(lines)
    in_headers = false
    lines.each_with_index {|line, i|
        if line =~ /^\S[^\:]+\:( .*?)?$/
            in_headers = true
        elsif in_headers === true
            return i
        else
            return false
        end
    }
end

input = STDIN.read

links=input.scan(/\[([^\]]+)\]\((https?:\/\/[^\)]+)\)/)
refs = input.scan(/^\[([^\]]+)\]: (\S+)$/)
lines = input.split("\n")

bottom = lines[0..-1].join("\n").gsub(/^\[([^\]]+)\]: (\S+)\n?/,'')

norepeat = []
norepeatlinks = []
output = []

refs.each {|ref|
    name = ref[0]
    puts "name: " + name
    next if norepeatlinks.include? ref[1]
    while norepeat.include? name
        if name =~ / ?[0-9]$/
            name.next!
        else 
            name = name + " 2"
        end
    end
    output << {'orig' => ref[0], 'title' => name, 'link' => ref[1]}
    norepeat.push name
    norepeatlinks.push ref[1]
}

links.each {|link|
    name = mmd_linkname(link[0])
    url = link[1]
    next if norepeatlinks.include? url
    while norepeat.include? name
        if name =~ / ?[0-9]$/
            name.next!
        else 
            name = name + " 2"
        end
    end
    output << {'orig' => url, 'title' => name, 'link' => url }
    norepeat.push name
    norepeatlinks.push url
}
output = output.sort {|a,b| a['title'] <=> b['title']}
o = []

output.each_with_index { |x,i| 
    o.push("[#{x['title']}]: #{x['link']}")
    bottom = bottom.gsub(/\((#{e_sh x['orig']}|#{e_sh x['link']})\)/,"[#{x['title']}]").gsub(/\[#{e_sh x['orig']}\]/,"[#{x['title']}]")
}
puts bottom + "\n\n#{o.join("\n")}\n"