qupzilla_github_fix.js

// Copyright alket@megaglest.org CC0 Universal
// ==UserScript==
// @name        QupZilla Github Fix
// @namespace   qupzilla_github_fix
// @include     https://github.com/*
// @version     0.1
// @require     https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js
// ==/UserScript==

var html_list = "";
var item_title = "";
var item_href = "";

GM_addStyle(".select-menu-filters {max-height:400px;overflow-y:scroll;}#qpf-list li { list-style-type:none;} #qpf-list li a {display:block;padding:6px;text-decoration:none;color:#666;} #qpf-list a:hover {background:#4078C0;color:#fff;}#qpf-list .selected{font-weight:bold;color:#4078C0;} .qpf-span {padding:6px;font-weight:bold;color:#000;}");

$(document).ready(function() {
	html_list += '<span class="qpf-span">Branches</span><ul id="qpf-list">';
	$('*[data-tab-filter="branches"] a').each(function( index ) {
		item_title = $(this).text();
		item_title = item_title.replace(/\s/g, '');
		item_href = $(this).attr("href");
		if ( $( this ).hasClass("selected")) {
			html_list += '<li><a class="selected" href="'+item_href+'">'+item_title+'</a></li>';
		} else {
			html_list += '<li><a href="'+item_href+'">'+item_title+'</a></li>';
		}
		
	});
	html_list += "</ul>";
	html_list += '<span class="qpf-span">Tags</span><ul id="qpf-list">';
	$('*[data-tab-filter="tags"] a').each(function( index ) {
		item_title = $(this).text();
		item_title = item_title.replace(/\s/g, '');
		item_href = $(this).attr("href");
		if ( $( this ).parent().hasClass("selected")) {
			html_list += '<li><a class="selected" href="'+item_href+'">'+item_title+'</a></li>';
		} else {
			html_list += '<li><a href="'+item_href+'">'+item_title+'</a></li>';
		}
		
	});
	html_list += "</ul>";
	$('.select-menu-filters').html(html_list);
});

This script is incorrect, you shouldn't use $(document).ready(function() instead you should set @run-at document-end (http://wiki.greasespot.net/Metadata_Block#.40run-at).

Thanks