See: http://css-tricks.com/forums/topic/wordpress-what-do-you-include-in-your-functions-php-file/

functions.php

<?php
/**
 * ----------------------------------------
 *  Adds template name, as class, on the body
 *  @return Array
 * ----------------------------------------
 */
add_filter('body_class', 'the_fresh_class_themer');
function the_fresh_class_themer($classes = '')
{
    global $template;
    $classes[] = substr(basename($template), 0, -4);
    return $classes;
}
/**
 * ----------------------------------------
 *  Displays, front-end, which template is being used
 *  @return String
 * ----------------------------------------
 */
add_action( 'wp_head', 'init_template_display' );
function init_template_display()
{
    if ( current_user_can('manage_options') ) {
        global $template;
        echo '<div class="cf" style="padding:24px;text-align:center;"><b>Using Template, <em>init_template_display();</em><br></b><code>'.$template.'</code></div>';
    }
}
/**
 * ----------------------------------------
 *  Displays all WordPress Constants defined
 *  @return String
 * ----------------------------------------
 */
add_action( 'wp_head', 'init_display_all_constants' );
function init_display_all_constants()
{
    if ( current_user_can('manage_options') ) {
        echo '<div class="cf" style="padding:24px;text-align:center;"><b>All Defined Constants</b>';
        var_dump(@get_defined_constants());
        echo '</div>';
    }
}
/**
 * ----------------------------------------
 *  Theme Clean Up
 * ----------------------------------------
 */
add_action('init', 'init_theme_clean_up');
function init_theme_clean_up()
{
    remove_action( 'wp_head', 'feed_links_extra', 3 );
    remove_action( 'wp_head', 'rsd_link' );
    remove_action( 'wp_head', 'wlwmanifest_link' );
    remove_action( 'wp_head', 'index_rel_link' );
    remove_action( 'wp_head', 'parent_post_rel_link', 10, 0 );
    remove_action( 'wp_head', 'start_post_rel_link', 10, 0 );
    remove_action( 'wp_head', 'adjacent_posts_rel_link_wp_head', 10, 0 );
    remove_action( 'wp_head', 'wp_generator' );
    add_filter( 'show_admin_bar', '__return_false' );
}
/**
 * ----------------------------------------
 *  Theme Support
 * ----------------------------------------
 */
add_action( 'after_setup_theme', 'init_theme_support' );
function init_theme_support()
{
    add_post_type_support('page', ['excerpt']);
    add_theme_support('automatic-feed-links');
    add_theme_support('post-formats', [
        'aside',
        'gallery',
        'link',
        'image',
        'quote',
        'status',
        'video',
        'audio',
        'chat'
    ]);
    add_theme_support('menus');
    register_nav_menu('head-navigation', __( 'Header Navigation'));
    register_nav_menu('side-navigation', __( 'Sidebar Navigation'));
    register_nav_menu('foot-navigation', __( 'Footer Navigation'));
    add_theme_support('post-thumbnails');
    set_post_thumbnail_size(125, 125, true);
    add_image_size('brand-300', 300, 100, true );
    add_theme_support('custom-background');
    add_theme_support('html5', ['search-form', 'comment-form', 'comment-list']);
}
/**
 * ----------------------------------------
 *  Nicely Formatted Title
 *  @return String
 * ----------------------------------------
 */
add_filter( 'wp_title', 'init_nicely_formatted_titles', 10, 2 );
function init_nicely_formatted_titles( $title, $sep )
{
    global $paged, $page;
    if ( is_feed() ) { return $title; }
    $title .= get_bloginfo( 'name' );
    $site_description = get_bloginfo( 'description', 'display' );
    if ( $site_description && ( is_home() || is_front_page() ) ) {
        $title = "$title $sep $site_description";
    }
    if ( $paged >= 2 || $page >= 2 ) {
        $title = "$title $sep " . sprintf( __( 'Page %s' ), max( $paged, $page ) );
    }
    return $title;
}
/**
 * ----------------------------------------
 *  Clear Administration Panel
 * ----------------------------------------
 */
add_action( 'admin_menu', 'init_disable_dash_components' );
function init_disable_dash_components()
{
    remove_meta_box( 'dashboard_right_now', 'dashboard', 'core' );
    remove_meta_box( 'dashboard_recent_comments', 'dashboard', 'core' );
    remove_meta_box( 'dashboard_incoming_links', 'dashboard', 'core' );
    remove_meta_box( 'dashboard_plugins', 'dashboard', 'core' );
    remove_meta_box( 'dashboard_quick_press', 'dashboard', 'core' );
    remove_meta_box( 'dashboard_recent_drafts', 'dashboard', 'core' );
    remove_meta_box( 'dashboard_primary', 'dashboard', 'core' );
    remove_meta_box( 'dashboard_secondary', 'dashboard', 'core' );
}
/**
 * ----------------------------------------
 *  Remove dimensions from images, responsive images
 *  @return String
 * ----------------------------------------
 */
add_filter( 'post_thumbnail_html', 'init_remove_wh_responsive_images', 10 );
add_filter( 'image_send_to_editor', 'init_remove_wh_responsive_images', 10 );
function init_remove_wh_responsive_images($html)
{
    return preg_replace( '/(width|height)=\"\d*\"\s/', "", $html );
}
/**
 * ----------------------------------------
 *  Load Administration Scripts & Styles
 * ----------------------------------------
 */
add_action('admin_head', 'init_admin_scripts_styles');
function init_admin_scripts_styles()
{
    wp_enqueue_style( 'admin', get_template_directory_uri() . '/css/admin.min.css', [], '1.0', 'all' );
}
/**
 * ----------------------------------------
 *  Front-End Scripts & Styles
 * ----------------------------------------
 */
add_action( 'wp_enqueue_scripts', 'init_theme_scripts_styles' );
function init_theme_scripts_styles()
{
    global $wp_styles;
    # scripts
    wp_enqueue_script( 'jquery' );
    # wp_enqueue_script( $handle, $src, $deps, $ver, $in_footer );
    wp_enqueue_script( 'main', get_template_directory_uri() . '/js/master.min.js', ['jquery'], '1.0', true );
    # styles
    # wp_enqueue_style( $handle, $src, $deps, $ver, $media );
    wp_enqueue_style( 'main', get_template_directory_uri() . '/css/master.min.css', [], '1.0', 'all' );
}
/**
 * ----------------------------------------
 *  Turn current_* to active classes on wp_nav_menu()
 *  @return String
 * ----------------------------------------
 */
add_filter ('wp_nav_menu','init_change_current_nav_classes');
function init_change_current_nav_classes($text)
{
    $replace = [
        'current_page_item' => 'active',
        'current_page_parent' => 'active',
        'current_page_ancestor' => 'active',
    ];
    return str_replace(array_keys($replace), $replace, $text);
}
/**
 * ----------------------------------------
 *  Custom Administration Footer Credit
 *  @return String
 * ----------------------------------------
 */
add_filter('admin_footer_text', 'init_custom_footer_info');
function init_custom_footer_info()
{
    echo '<a href="http://alenabdula.com/" target="_blank">Alen Abdula</a>';
}
/**
 * ----------------------------------------
 *  Remove Top-Left WordPress Logo
 * ----------------------------------------
 */
add_action('wp_before_admin_bar_render', 'init_remove_top_left_wp_logo', 0);
function init_remove_top_left_wp_logo()
{
    global $wp_admin_bar;
    $wp_admin_bar->remove_menu('wp-logo');
}
/**
 * ----------------------------------------
 *  Widgets
 * ----------------------------------------
 */
add_action( 'widgets_init', 'init_theme_widgets' );
function init_theme_widgets()
{
    register_sidebar([
        'name' => __( 'Sidebar One'),
        'id' => 'sidebar-1',
        'description'   => __('Sidebar One allows you to include widgets!'),
        'before_widget' => '<div id="%1$s" class="widget %2$s">',
        'after_widget'  => '</div>',
        'before_title'  => '<h2 class="widget-title">',
        'after_title'   => '</h2>',
        ]);
    register_sidebar([
        'name' => __( 'Sidebar Two'),
        'id' => 'sidebar-2',
        'description'   => __('Sidebar Two allows you to include widgets!'),
        'before_widget' => '<div id="%1$s" class="widget %2$s">',
        'after_widget'  => '</div>',
        'before_title'  => '<h2 class="widget-title">',
        'after_title'   => '</h2>',
        ]);
}
/**
 * ----------------------------------------
 *  Remove Menu Items
 * ----------------------------------------
 */
add_action('admin_menu', 'init_remove_admin_menu_items', 102);
function init_remove_admin_menu_items()
{
    global $submenu;
    $remove_menu_page_collection = [
        // 'index.php',                    // Dashboard
        // 'edit.php',                     // Posts
        // 'upload.php',                   // Media
        // 'edit.php?post_type=page',      // Pages
        // 'edit-comments.php',            // Comments
        // 'themes.php',                   // Appearance
        // 'plugins.php',                  // Plugins
        // 'users.php',                    // Users
        // 'tools.php',                    // Tools
        // 'options-general.php',          // Settings
        // 'edit.php?post_type=acf',       // Advanced Custom Fields
    ];
    foreach ($remove_menu_page_collection as $collection) {
        # remove_menu_page( $menu-slug );
        remove_menu_page($collection);
    }
    $remove_submenu_page_collection = [
        // 'themes.php' => 'theme-editor.php',
        // 'index.php' => 'update-core.php',
    ];
    foreach ($remove_submenu_page_collection as $key => $value) {
        # remove_submenu_page( $menu_slug, $submenu_slug );
        remove_submenu_page( $key, $value );
    }
}
/**
 * ----------------------------------------
 *  Unregistering Default Widgets
 * ----------------------------------------
 */
add_action('widgets_init', 'init_unregister_default_widgets');
function init_unregister_default_widgets()
{
    $widgets_collection = [
        'WP_Widget_Pages',
        'WP_Widget_Calendar',
        'WP_Widget_Archives',
        'WP_Widget_Links',
        'WP_Widget_Meta',
        'WP_Widget_Search',
        'WP_Widget_Text',
        'WP_Widget_Categories',
        'WP_Widget_Recent_Posts',
        'WP_Widget_Recent_Comments',
        'WP_Widget_RSS',
        'WP_Widget_Tag_Cloud',
        'WP_Nav_Menu_Widget',
        'Twenty_Eleven_Ephemera_Widget',
    ];
    foreach ($widgets_collection as $item) {
        unregister_widget($item);
    }
}
/**
 * ----------------------------------------
 *  Custom Login
 *  @return String
 * ----------------------------------------
 */
add_action('login_head', 'init_custom_login_branding');
function init_custom_login_branding()
{
    $path = get_template_directory_uri() . '/img/wp_admin_login_branding.png';
    echo '<style>body{background-color:#dff0c8!important;}.login h1 a{background-image:url('.$path.')!important;background-size:125px 62px!important;width:125px!important;height:62px!important;}</style>';
}
/**
 * ----------------------------------------
 *  Custom Login URL
 *  @return String
 * ----------------------------------------
 */
add_filter( 'login_headerurl', 'init_custom_login_url' );
function init_custom_login_url()
{
    return get_bloginfo('url', 'raw');
}
/**
 * ----------------------------------------
 *  Custom Login Title
 *  @return String
 * ----------------------------------------
 */
add_filter('login_headertitle', 'init_custom_login_title');
function init_custom_login_title()
{
   return get_option('blogname');
}
/**
 * ----------------------------------------
 *  Remove <p> around images
 *  see: http://css-tricks.com/snippets/wordpress/remove-paragraph-tags-from-around-images/
 *  @return String
 * ----------------------------------------
 */
add_filter('the_content', 'init_remove_p_tags_around_images');
function init_remove_p_tags_around_images($content)
{
   return preg_replace('/<p>\s*(<a .*>)?\s*(<img .* \/>)\s*(<\/a>)?\s*<\/p>/iU', '\1\2\3', $content);
}