reference_link.py

import sublime, sublime_plugin

class ReferenceLinkInputHandler(sublime_plugin.TextInputHandler):

    def placeholder(self):
        return "Type a link"


class ReferenceLinkCommand(sublime_plugin.TextCommand):

    def run(self, edit, reference_link):
        link_number = 1
        ref_links = self.view.find_by_selector("meta.link.reference.def.markdown")
        pos = self.view.sel()[0]
        entered_link = "https://" + reference_link

        selected_text = self.view.substr(self.view.sel()[0])

        # If there is no reference link.
        if len(ref_links) == 0:
            self.view.replace(edit, pos, self.link_template(selected_text, link_number))
            self.view.insert(edit, self.view.size(), "\n\n" + self.reference_template(link_number, entered_link))
            return

        # Find the largest reference link number.
        max_link_num = 0
        for i in ref_links:
            region = sublime.Region(i.begin(), i.end())
            link_num = self.view.substr(region).split(":", 1)[0][1]
            if int(link_num) > int(max_link_num):
                max_link_num = int(link_num)

        # If the reference link is same as one already present.
        for i in ref_links:
            region = sublime.Region(i.begin(), i.end())
            actual_link = self.view.substr(region).split(":", 1)[1].strip()
            link_num = self.view.substr(region).split(":", 1)[0][1]
            if actual_link == entered_link:
                self.view.replace(edit, pos, self.link_template(selected_text, link_num))
                return

        self.view.replace(edit, pos, self.link_template(selected_text, max_link_num + 1))
        self.view.insert(edit, self.view.size(),  "\n" + self.reference_template(max_link_num + 1, entered_link))


    def input(self, args):
        if args is not None:
            return ReferenceLinkInputHandler()

    def input_description(self):
        return "https://"

    @staticmethod
    def reference_template(link_number, link):
        return "[{}]: {}".format(link_number, link)

    @staticmethod
    def link_template(text, link_number):
        if text == "":
            return "[Enter description here][{}]".format(link_number)
        return "[{}][{}]".format(text, link_number)

Yep, Your code was a great starting point for me. Thank You.