I've made a couple of fixes to make this work again. While I don't fork and ask for a merge, here it is a copy of my script for convenience, the modifications are indicated with comments. The matches of sites has been revised as well. 

    // ==UserScript==
    // @name           stackoverflow-comment-reply
    // @namespace      stackapps
    // @description    Add "reply" links to comments
    // @version        1.1c
    // @match          *://*.askubuntu.com/*
    // @match          *://*.mathoverflow.net/*
    // @match          *://*.serverfault.com/*
    // @match          *://*.stackapps.com/*
    // @match          *://*.stackexchange.com/*
    // @match          *://*.stackoverflow.com/*
    // @match          *://*.superuser.com/*
    // @match          *://area51.stackexchange.com/proposals/*
    // @author         Benjamin Dumke-von der Ehe
    // ==/UserScript==
    
    /* MOD: don't run if not SE and user not logged in */
    if (!window.StackExchange || window.StackExchange.options.user.isAnonymous )
        return;
    
    // Thanks to Shog9 for this idea for making the script work in both
    // Chrome and Firefox:
    // http://meta.stackoverflow.com/questions/46562
    function with_jquery(f) {
        var script = document.createElement("script");
        script.type = "text/javascript";
        script.textContent = "(" + f.toString() + ")(jQuery)";
        document.body.appendChild(script);
    };
    
    with_jquery(function($) {
    
        $(document).ajaxComplete(function(){
            setTimeout(function () {
                $(".comments").each(put_reply_links);
            }, 100);
        });
    
        // event handler for a click on the reply links
        function reply() {
            /* MOD: changed the following 2 lines to detect the new Add Comment link */
            var commentlinkId = $(this).closest(".comments").next().attr("id");
            var commentlink = $('#'+commentlinkId + ' a.js-add-link')[0].click();
            var username = goodify($(this).prev().text().replace(/♦/, ""))
            var formid = commentlinkId.replace(/^.*-(\d+)$/, "add-comment-$1");
            var ta = $("#" + formid + " textarea")[0];
            var start = ta.selectionStart;
            var end = ta.selectionEnd;
            var shift = username.length + 3;
            ta.value = "@" + username + ": " + ta.value;
            ta.focus();
            ta.selectionStart = start + shift;
            ta.selectionEnd = end + shift;
        };
    
        function put_reply_links() {
            $(this).find(".comment:not(:has(.reply-link)) .comment-user").each(function () {
                /* MOD: // changed click by on(click) */
                $("<span class='reply-link' style='cursor:pointer;opacity:0.3' title='reply'> &crarr;</span>").on('click',reply).insertAfter(this); 
            });
        }
    
        $(".comments").each(put_reply_links);
    
        function goodify(s) {
            return s.replace(/ +/g, "");
        }   
    });