functions.php

<?php

// Theme Setup (based on twentythirteen: http://make.wordpress.org/core/tag/twentythirteen/)
function html5reset_setup() {
    load_theme_textdomain('html5reset', get_template_directory() . '/languages');
    add_theme_support('automatic-feed-links');
    add_theme_support('structured-post-formats', array('link', 'video'));
    register_nav_menu('primary', __('Navigation Menu', 'html5reset'));
    add_theme_support('post-thumbnails');
    add_image_size('bookmark-icon', 150, 150, false);
}

add_action('after_setup_theme', 'html5reset_setup');
// Scripts & Styles (based on twentythirteen: http://make.wordpress.org/core/tag/twentythirteen/)
add_action('wp_enqueue_scripts', 'html5reset_scripts_styles');

function html5reset_scripts_styles() {
    global $wp_styles;
}

if (!is_admin()) {
    add_action("wp_enqueue_scripts", "my_jquery_enqueue", 11);
}

function my_jquery_enqueue() {
    wp_deregister_script('jquery');
    wp_register_script('jquery', "http" . ($_SERVER['SERVER_PORT'] == 443 ? "s" : "") . "://ajax.googleapis.com/ajax/libs/jquery/1.9.1/jquery.min.js?ver=3.7.1", false, null);
    wp_enqueue_script('jquery');
}

if (!is_admin()) {
    add_action("wp_enqueue_scripts", "my_fancybox_enqueue", 11);
}

function my_fancybox_enqueue() {
    wp_deregister_script('fancybox');
    wp_register_script('fancybox', get_template_directory_uri() . '/js/jquery.fancybox.pack.js', false, null);
    wp_enqueue_script('fancybox');
}

// Custom Logo
function sp_login_logo() {
    ?>
    <style type="text/css">
        body.login div#login h1 a {
            background-image: url(<?php echo get_template_directory_uri(); ?>/img/logo.png);
            padding-bottom: 30px;
            background-size: 267px 46px;
            width: 267px;
            height: 46px;
        }
    </style>
    <?php
}

add_action('login_enqueue_scripts', 'sp_login_logo');
// Dash Cleanup
add_action('wp_dashboard_setup', 'dashboard_cleanup');

function dashboard_cleanup() {
    remove_meta_box('dashboard_primary', 'dashboard', 'side');      //WordPress.com Blog
    remove_meta_box('dashboard_secondary', 'dashboard', 'side');      //Other WordPress News
    remove_meta_box('dashboard_incoming_links', 'dashboard', 'normal');    //Incoming Links
    remove_meta_box('dashboard_plugins', 'dashboard', 'normal');    //Plugins
}

// Enable Links
add_filter('pre_option_link_manager_enabled', '__return_true');

// Register Bookmarks Post Type
function bookmarks() {

    $labels = array(
        'name' => 'Bookmarks',
        'singular_name' => 'Bookmark',
        'menu_name' => 'Bookmarks',
        'parent_item_colon' => 'Parent Bookmark:',
        'all_items' => 'All Bookmarks',
        'view_item' => 'View Bookmark',
        'add_new_item' => 'Add New Bookmark',
        'add_new' => 'New Bookmark',
        'edit_item' => 'Edit Bookmark',
        'update_item' => 'Update Bookmark',
        'search_items' => 'Search Bookmarks',
        'not_found' => 'No Bookmarks found',
        'not_found_in_trash' => 'No Bookmarks found in Trash',
    );
    $args = array(
        'label' => 'bookmark',
        'description' => 'Create your custom Bookmarks',
        'labels' => $labels,
        'supports' => array('title', 'thumbnail', 'page-attributes'),
        'taxonomies' => array('category'),
        'hierarchical' => true,
        'public' => true,
        'show_ui' => true,
        'show_in_menu' => true,
        'show_in_nav_menus' => true,
        'show_in_admin_bar' => true,
        'menu_position' => 5,
        'can_export' => true,
        'has_archive' => true,
        'exclude_from_search' => false,
        'publicly_queryable' => true,
        'capability_type' => 'post',
    );
    register_post_type('bookmark', $args);
}

// Hook into the 'init' action
add_action('init', 'bookmarks', 0);
// Custom Meta Boxes
add_action('add_meta_boxes', 'cd_meta_box_add');

function cd_meta_box_add() {
    add_meta_box('startpress', 'Start Press Options', 'cd_meta_box_cb', 'bookmark', 'normal', 'high');
}

function cd_meta_box_cb($post) {
    $values = get_post_custom($post->ID);
    $sp_url = isset($values['sp_url']) ? esc_attr($values['sp_url'][0]) : '';
    $sp_new = isset($values['sp_new']) ? esc_attr($values['sp_new'][0]) : '';
    $sp_modal = isset($values['sp_modal']) ? esc_attr($values['sp_modal'][0]) : '';
    $sp_anon = isset($values['sp_anon']) ? esc_attr($values['sp_anon'][0]) : '';
    wp_nonce_field('my_meta_box_nonce', 'meta_box_nonce');
    ?>
    <h3>
        <label for="sp_url">Website Address</label>
    </h3>
    <p>
        <input type="text" name="sp_url" id="sp_url" size="50" value="<?php echo $sp_url; ?>" placeholder="http://" />
    </p>
    <h3>
        <label for="sp_url">Settings</label>
    </h3>
    <p>
        <input type="checkbox" name="sp_new" id="sp_new" <?php checked($sp_new, 'on'); ?> />
        <label for="sp_new"> Open In New Window</label>
    </p>
    <p>
        <input type="checkbox" name="sp_modal" id="sp_modal" <?php checked($sp_modal, 'on'); ?> />
        <label for="sp_modal"> Open In Modal</label>
    </p>
    <p>
        <input type="checkbox" name="sp_anon" id="sp_anon" <?php checked($sp_anon, 'on'); ?> />
        <label for="sp_anon"> Derefer</label>
    </p>
    <?php
}

add_action('save_post', 'cd_meta_box_save');

function cd_meta_box_save($post_id) {
    // Bail if we're doing an auto save
    if (defined('DOING_AUTOSAVE') && DOING_AUTOSAVE)
        return;

    // if our nonce isn't there, or we can't verify it, bail
    if (!isset($_POST['meta_box_nonce']) || !wp_verify_nonce($_POST['meta_box_nonce'], 'my_meta_box_nonce'))
        return;

    // if our current user can't edit this post, bail
    if (!current_user_can('edit_post'))
        return;

    // now we can actually save the data
    $allowed = array(
        'a' => array(// on allow a tags
            'href' => array() // and those anchords can only have href attribute
        )
    );

    // Probably a good idea to make sure your data is set
    if (isset($_POST['sp_url']))
        update_post_meta($post_id, 'sp_url', wp_kses($_POST['sp_url'], $allowed));

    // This is purely my personal preference for saving checkboxes
    $chk = ( isset($_POST['sp_new']) && $_POST['sp_new'] ) ? 'on' : 'off';
    update_post_meta($post_id, 'sp_new', $chk);
    $chk2 = ( isset($_POST['sp_modal']) && $_POST['sp_modal'] ) ? 'on' : 'off';
    update_post_meta($post_id, 'sp_modal', $chk2);
    $chk3 = ( isset($_POST['sp_anon']) && $_POST['sp_anon'] ) ? 'on' : 'off';
    update_post_meta($post_id, 'sp_anon', $chk3);
}

// Order Categories by Wessley Roche
function wpguy_category_order_init() {

    function wpguy_category_order_menu() {
        if (function_exists('add_submenu_page')) {
            add_submenu_page("edit.php?post_type=bookmark", 'Order', 'Order', 'Editor', "wpguy_category_order_options", 'wpguy_category_order_options');
        }
    }

    function wpguy_category_order_scriptaculous() {
        if (isset($_GET['page']) && $_GET['page'] == "wpguy_category_order_options") {
            wp_enqueue_script('scriptaculous');
        }
    }

    add_action('admin_head', 'wpguy_category_order_options_head');
    add_action('admin_menu', 'wpguy_category_order_menu');
    add_action('admin_menu', 'wpguy_category_order_scriptaculous');

    add_filter('get_terms', 'wpguy_category_order_reorder', 10, 3);

    // This is the main function. It's called every time the get_terms function is called.
    function wpguy_category_order_reorder($terms, $taxonomies, $args) {

        // No need for this if we're in the ordering page.
        if (isset($_GET['page']) && $_GET['page'] == "wpguy_category_order_options") {
            return $terms;
        }

        // Apply to categories only and only if they're ordered by name.
        if ($taxonomies[0] == "category" && $args['orderby'] == 'name') { // You may change this line for: `if($taxonomies[0] == "category" && $args['orderby'] == 'custom'){` if you wish to still be able to order by name.
            $options = get_option("wpguy_category_order");

            if (!empty($options)) {

                // Put all the order strings together
                $master = "";
                foreach ($options as $id => $option) {
                    $master .= $option . ",";
                }

                $ids = explode(",", $master);

                // Add an 'order' item to every category
                $i = 0;
                foreach ($ids as $id) {
                    if ($id != "") {
                        foreach ($terms as $n => $category) {
                            if (is_object($category) && $category->term_id == $id) {
                                $terms[$n]->order = $i;
                                $i++;
                            }
                        }
                    }

                    // Add order 99999 to every category that wasn't manually ordered (so they appear at the end). This just usually happens when you've added a new category but didn't order it.
                    foreach ($terms as $n => $category) {
                        if (is_object($category) && !isset($category->order)) {
                            $terms[$n]->order = 99999;
                        }
                    }
                }

                // Sort the array of categories using a callback function
                usort($terms, "wpguy_category_order_compare");
            }
        }

        return $terms;
    }

    // Compare function. Used to order the categories array.
    function wpguy_category_order_compare($a, $b) {

        if ($a->order == $b->order) {

            if ($a->name == $b->name) {
                return 0;
            } else {
                return ($a->name < $b->name) ? -1 : 1;
            }
        }

        return ($a->order < $b->order) ? -1 : 1;
    }

    function wpguy_category_order_options() {
        if (isset($_GET['childrenOf'])) {
            $childrenOf = $_GET['childrenOf'];
        } else {
            $childrenOf = 0;
        }


        $options = get_option("wpguy_category_order");
        $order = $options[$childrenOf];


        if (isset($_GET['submit'])) {
            $options[$childrenOf] = $order = $_GET['category_order'];
            update_option("wpguy_category_order", $options);
            $updated = true;
        }

        // Get the parent ID of the current category and the name of the current category.
        $allthecategories = get_categories("hide_empty=0");
        if ($childrenOf != 0) {
            foreach ($allthecategories as $category) {
                if ($category->cat_ID == $childrenOf) {
                    $father = $category->parent;
                    $current_name = $category->name;
                }
            }
        }

        // Get only the categories belonging to the current category
        $categories = get_categories("hide_empty=0&child_of=$childrenOf");

        // Order the categories.
        if ($order) {
            $order_array = explode(",", $order);

            $i = 0;

            foreach ($order_array as $id) {
                foreach ($categories as $n => $category) {
                    if (is_object($category) && $category->term_id == $id) {
                        $categories[$n]->order = $i;
                        $i++;
                    }
                }


                foreach ($categories as $n => $category) {
                    if (is_object($category) && !isset($category->order)) {
                        $categories[$n]->order = 99999;
                    }
                }
            }

            usort($categories, "wpguy_category_order_compare");
        }
        ?>

        <div class='wrap'>

        <?php if (isset($updated) && $updated == true): ?>
                <div id="message" class="fade updated"><p>Changes Saved.</p></div>
            <?php endif; ?>

            <form action="<?php bloginfo("wpurl") ?>/wp-admin/edit.php" class="GET">
                <input type="hidden" name="post_type" value="bookmark" />
                <input type="hidden" name="page" value="wpguy_category_order_options" />
                <input type="hidden" id="category_order" name="category_order" size="500" value="<?php echo $order; ?>">
                <input type="hidden" name="childrenOf" value="<?php echo $childrenOf; ?>" />
                <h2>Order</h2>
        <?php if ($childrenOf != 0): ?>
                    <p><a href="<?php bloginfo("wpurl"); ?>/wp-admin/edit.php?page=wpguy_category_order_options&amp;childrenOf=<?php echo $father; ?>">&laquo; Back</a></p>
                    <h3><?php echo $current_name; ?></h3>
        <?php else: ?>
                <?php endif; ?>

                <div id="container">
                    <div id="order">
        <?php
        foreach ($categories as $category) {

            if ($category->parent == $childrenOf) {

                echo "<div id='item_$category->cat_ID' class='lineitem'>";
                if (get_categories("hide_empty=0&child_of=$category->cat_ID")) {
                    echo "<span class=\"childrenlink\"><a href=\"" . get_bloginfo("wpurl") . "/wp-admin/edit.php?page=wpguy_category_order_options&childrenOf=$category->cat_ID\">More &raquo;</a></span>";
                }
                echo "<h4>$category->name</h4>";
                echo "</div>\n";
            }
        }
        ?>
                    </div>
                    <p>Drag to change order</p>
                    <p class="submit"><input type="submit" name="submit" Value="Save Order"></p>
                </div>
            </form>
        </div>

        <?php
    }

    // The necessary CSS and Javascript
    function wpguy_category_order_options_head() {
        if (isset($_GET['page']) && $_GET['page'] == "wpguy_category_order_options") {
            ?>
            <style>
                #container{
                    list-style: none;
                    width: 225px;
                }

                #order{
                }

                .childrenlink{
                    float: right;
                    font-size: 12px;
                }

                .lineitem {
                    background-color: #ddd;
                    color: #000;
                    margin-bottom: 5px;
                    padding: .5em 1em;
                    width: 200px;
                    font-size: 13px;
                    -moz-border-radius: 3px;
                    -khtml-border-radius: 3px;
                    -webkit-border-radius: 3px;
                    border-radius: 3px;
                    cursor: move;
                }

                .lineitem h4{
                    font-weight: bold;
                    margin: 0;
                }
            </style>

            <script language="JavaScript">
                window.onload = function () {
                    Sortable.create('order', {tag: 'div', onChange: function () {
                            refreshOrder();
                        }});

                    function refreshOrder() {
                        $("category_order").value = Sortable.sequence('order');
                    }
                }
            </script>
            <?php
        }
    }

}

add_action('init', 'wpguy_category_order_init');
// Sidebar
add_action('widgets_init', 'spsidebar');

function spsidebar() {
    register_sidebar(
            array(
                'id' => 'spsidebar',
                'name' => __('Sidebar'),
                'before_widget' => '<div id="%1$s" class="widget %2$s">',
                'after_widget' => '</div>',
                'before_title' => '<h3 class="widget-title">',
                'after_title' => '</h3>'
            )
    );
}

// Navigation
function post_navigation() {
    echo '<div class="navigation">';
    echo '	<div class="next-posts">' . get_next_posts_link('&laquo; Older Entries') . '</div>';
    echo '	<div class="prev-posts">' . get_previous_posts_link('Newer Entries &raquo;') . '</div>';
    echo '</div>';
}

// Posted On
function posted_on() {
    printf(__('<span class="sep">Posted </span><a href="%1$s" title="%2$s" rel="bookmark"><time class="entry-date" datetime="%3$s" pubdate>%4$s</time></a> by <span class="byline author vcard">%5$s</span>', ''), esc_url(get_permalink()), esc_attr(get_the_time()), esc_attr(get_the_date('c')), esc_html(get_the_date()), esc_attr(get_the_author())
    );
}

//Move plugins to footer
function footer_enqueue_scripts() {
    remove_action('wp_head', 'wp_print_scripts');
    remove_action('wp_head', 'wp_print_head_scripts', 9);
    remove_action('wp_head', 'wp_enqueue_scripts', 1);
    add_action('wp_footer', 'wp_print_scripts', 5);
    add_action('wp_footer', 'wp_enqueue_scripts', 5);
    add_action('wp_footer', 'wp_print_head_scripts', 5);
}

add_action('after_setup_theme', 'footer_enqueue_scripts');
?>