WordPress functions.php file with various cleanup, security, performance and helper functions. Obviously requires customisation as per theme needs.

functions.php

<?php

function im_setup() {

// ++++++++++++++++ REGISTER THEME OBJECTS ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	// Register and enqueue Javascript 
	function im_js() {

		// Modernizr
		wp_register_script( 'modernizr-script', get_template_directory_uri() . '/_inc/modernizr.min.js', false, '1.0', false );
		wp_enqueue_script( 'modernizr-script' );

		// jQuery
		wp_deregister_script( 'jquery' );
		wp_register_script('jquery', get_template_directory_uri() . '/_inc/jquery.min.js', false, '2.0.0', true );
		wp_enqueue_script( 'jquery' );

		// Custom
		wp_register_script( 'im-script', get_template_directory_uri() . '/_inc/script.min.js', array('jquery'), false, '1.2', true );
		wp_enqueue_script( 'im-script' );

	}
	add_action( 'wp_enqueue_scripts', 'im_js' );


	// Register menu
	register_nav_menu( 'primary', 'Primary Menu' );


	// Register Feed Links, Post Formats, Custom Thumbnails, HTML5
	if ( function_exists( 'add_theme_support' ) ):
		add_theme_support( 'automatic-feed-links' );
		add_theme_support( 'post-formats', array( 'aside', 'image', 'link', 'quote', 'status' ) );
		add_theme_support( 'post-thumbnails' );
		add_theme_support( 'html5', array( 'comment-list', 'comment-form', 'search-form' ) );
	endif;


	// Register image sizes
	if ( function_exists( 'add_image_size' ) ):
		add_image_size( 'large', 800, 600 );
	endif;



// ++++++++++++++++ PERFORMANCE +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	// Enable GZIP compression
	if(extension_loaded("zlib") && (ini_get("output_handler") != "ob_gzhandler"))
	add_action('wp', create_function('', '@ob_end_clean();@ini_set("zlib.output_compression", 1);'));


	// Remove the version query string from scripts and styles - allows for better caching
	function im_remove_script_version( $src ){
		$parts = explode( '?', $src );
		return $parts[0];
	}
	add_filter( 'script_loader_src', 'im_remove_script_version', 15, 1 );
	add_filter( 'style_loader_src', 'im_remove_script_version', 15, 1 );


	// Prevents WordPress from testing SSL capability on domain.com/xmlrpc.php?rsd when XMLRPC not in use
	remove_filter('atom_service_url','atom_service_url_filter');


// ++++++++++++++++ SECURITY MODIFICATIONS ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	// Hide login form error messages
	add_filter('login_errors',create_function('$a', "return 'Error';"));


	// Remove WordPress version number
	function im_remove_wp_version() { return ''; }
	add_filter('the_generator', 'im_remove_wp_version');


	// Disable XMLRPC
	add_filter('xmlrpc_enabled', '__return_false');


// ++++++++++++++++ WP CLEANUP ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	// General Cleanup - removes unnecessary WordPress features
	remove_action( 'wp_head', 'feed_links_extra', 3 );
	remove_action( 'wp_head', 'feed_links', 2 );
	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' );
	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' );
	remove_action( 'wp_head', 'wp_shortlink_wp_head');


	// Unregister all default WP Widgets
	function im_unregister_default_wp_widgets() {
		unregister_widget('WP_Widget_Pages');
		unregister_widget('WP_Widget_Calendar');
		unregister_widget('WP_Widget_Archives');
		unregister_widget('WP_Widget_Links');
		unregister_widget('WP_Widget_Meta');
		unregister_widget('WP_Widget_Search');
		unregister_widget('WP_Widget_Text');
		unregister_widget('WP_Widget_Categories');
		unregister_widget('WP_Widget_Recent_Posts');
		unregister_widget('WP_Widget_Recent_Comments');
		unregister_widget('WP_Widget_RSS');
		unregister_widget('WP_Widget_Tag_Cloud');
	}
	add_action('widgets_init', 'im_unregister_default_wp_widgets', 1);


	// Cleanup Jetpack styles
	function im_remove_jetpack_styles(){
		wp_deregister_style('AtD_style'); 					// After the Deadline
		wp_deregister_style('jetpack-carousel'); 			// Carousel
		wp_deregister_style('grunion.css'); 				// Grunion contact form
		wp_deregister_style('the-neverending-homepage'); 	// Infinite Scroll
		wp_deregister_style('infinity-twentyten'); 			// Infinite Scroll - Twentyten Theme
		wp_deregister_style('infinity-twentyeleven'); 		// Infinite Scroll - Twentyeleven Theme
		wp_deregister_style('infinity-twentytwelve'); 		// Infinite Scroll - Twentytwelve Theme
		wp_deregister_style('noticons'); 					// Notes
		wp_deregister_style('post-by-email'); 				// Post by Email
		wp_deregister_style('publicize'); 					// Publicize
		wp_deregister_style('sharedaddy'); 					// Sharedaddy
		wp_deregister_style('sharing'); 					// Sharedaddy Sharing
		wp_deregister_style('stats_reports_css'); 			// Stats
		wp_deregister_style('jetpack-widgets'); 			// Widgets
	}
	add_action('wp_print_styles', 'im_remove_jetpack_styles');

	// Remove Jetpark Open Graph tags
	remove_action( 'wp_head', 'jetpack_og_tags');

	// Cleanup Jetpack scripts
	function im_dequeue_devicepx() {
		wp_dequeue_script( 'devicepx' );
	}
	add_action( 'wp_enqueue_scripts', 'im_dequeue_devicepx', 20 );


	// Remove inline style from Recent Comments widget
	function im_remove_recent_comments_style() {
		global $wp_widget_factory;
		remove_action( 'wp_head', array( $wp_widget_factory->widgets['WP_Widget_Recent_Comments'], 'recent_comments_style' ) );
	}
	add_action( 'widgets_init', 'im_remove_recent_comments_style' );


	// Set the maximum number of post revisions unless the constant is already set in wp-config.php
	if (!defined('WP_POST_REVISIONS')) define('WP_POST_REVISIONS', 5);


	// Disable Auto-Formatting in Content and Excerpt
	remove_filter( 'the_content', 'wpautop' );
	remove_filter( 'the_excerpt', 'wpautop' );


	// Disable Auto Linking of URLs in comments
	remove_filter('comment_text', 'make_clickable', 9);


	// Disable self-ping
	function im_self_ping( &$links ) {
		$home = get_option( 'home' );
		foreach ( $links as $l => $link )
			if ( 0 === strpos( $link, $home ) )
				unset($links[$l]);
	}
	add_action( 'pre_ping', 'im_self_ping' );


// ++++++++++++++++ ADMIN MODIFICATIONS +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	// Add visual editor stylesheet
	add_editor_style( 'editor-style.css' );


	// Change the default WordPress greeting in Admin
	function im_replace_howdy( $wp_admin_bar ) {
		$my_account=$wp_admin_bar->get_node('my-account');
		$newtitle = str_replace( 'Howdy,', 'Welcome, ', $my_account->title );
		$wp_admin_bar->add_node( array(
			'id' => 'my-account',
			'title' => $newtitle,
		) );
	}
	add_filter( 'admin_bar_menu', 'im_replace_howdy', 25 );


	// Add new Admin menu item "All Settings"
	function im_all_settings_link() {
		add_options_page(__('All Settings'), __('All Settings'), 'administrator', 'options.php');
	}
	add_action('admin_menu', 'im_all_settings_link');


	// Remove dashboard menu items
	function dashboard_tweaks() {
		global $wp_admin_bar;
		$wp_admin_bar->remove_menu('wp-logo');
		$wp_admin_bar->remove_menu('about');
		$wp_admin_bar->remove_menu('wporg');
		$wp_admin_bar->remove_menu('documentation');
		$wp_admin_bar->remove_menu('support-forums');
		$wp_admin_bar->remove_menu('feedback');
		$wp_admin_bar->remove_menu('view-site');
	}
	add_action( 'wp_before_admin_bar_render', 'dashboard_tweaks' );


// ++++++++++++++++ LOGIN MODIFICATIONS +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	// Custom login logo
	function im_custom_login_logo() {
		echo '<style type="text/css">
			.login #login { padding-top: 0;}
			.login h1 { width: 320px; height: 200px; }
			.login h1 a { background:url(' . get_template_directory_uri() . '/_img/login.png) 50% 50% no-repeat; background-size:contain; height: 200px; width: 320px; }
			</style>';
	}
	add_action('login_head', 'im_custom_login_logo');


	// Custom login URL
	function im_custom_login_url(){
		return ('http://imaginarymedia.com.au/');
	}
	add_filter('login_headerurl', 'im_custom_login_url');


	// Custom login URL Title Attribute
	function im_custom_login_title(){
		return ('Imaginary Media');
	}
	add_filter('login_headertitle', 'im_custom_login_title');


// ++++++++++++++++ CUSTOM POST TYPES +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //
	
	// Show Custom Post Types in search results
	function im_searchAll( $query ) {
		if ( $query->is_search ) { $query->set( 'post_type', array( 'site', 'plugin', 'theme', 'person' )); } 
		return $query;
	}
	add_filter( 'the_search_query', 'im_searchAll' );


	// Add Custom Post Types to the default RSS feed
	function im_custom_feed_request( $vars ) {
		if (isset($vars['feed']) && !isset($vars['post_type']))
			$vars['post_type'] = array( 'post', 'site', 'plugin', 'theme', 'person' );
		return $vars;
	}
	add_filter( 'request', 'im_custom_feed_request' );


// ++++++++++++++++ CUSTOM USER PROFILE FIELDS ++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	function im_custom_userfields( $contactmethods ) {

		$contactmethods['contact_phone'] 	= 'Contact Number';
		$contactmethods['social_fb'] 		= 'Facebook Profile';
		$contactmethods['social_tw'] 		= 'Twitter Profile';
		$contactmethods['social_gp'] 		= 'Google Plus Profile';
		
		return $contactmethods;
	}
	add_filter('user_contactmethods','im_custom_userfields',10,1);


// ++++++++++++++++ BASIC HELPER FUNCTIONS ++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //


	// Change the length of the default excerpt (number of words, default is 55)
	function im_excerpt_length($length) { 
		return 80;
	}
	add_filter('excerpt_length', 'im_excerpt_length');


	// Disable RSS feeds
	function im_disable_feed() {
		wp_die( __('No feed available,please visit our <a href="'. get_bloginfo('url') .'">homepage</a>!') );
	}
	add_action('do_feed', 'im_disable_feed', 1);
	add_action('do_feed_rdf', 'im_disable_feed', 1);
	add_action('do_feed_atom', 'im_disable_feed', 1);
	add_action('do_feed_rss', 'im_disable_feed', 1);
	add_action('do_feed_rss2', 'im_disable_feed', 1);


	// Gets the URL of the current page
	function get_url() {
		return (isset($_SERVER['HTTPS']) == 'on' ? 'https' : 'http').'://'.$_SERVER['HTTP_HOST'].$_SERVER['REQUEST_URI'];
	}


	// Allow custom MIME types to be uploaded
	function im_custom_upload_mimes ( $existing_mimes=array() ) {
		$existing_mimes['vcf'] = 'text/vcard';
		return $existing_mimes;
	}
	add_filter('upload_mimes', 'im_custom_upload_mimes');


	// Get post/page excerpt from ID
	function get_excerpt_by_id($post_id){
		$the_post = get_post($post_id);
		$the_excerpt = $the_post->post_content;
		$excerpt_length = 35;
		$the_excerpt = strip_tags(strip_shortcodes($the_excerpt));
		$words = explode(' ', $the_excerpt, $excerpt_length + 1);
		if(count($words) > $excerpt_length) :
			array_pop($words);
			array_push($words, '&hellip;');
			$the_excerpt = implode(' ', $words);
		endif;
		$the_excerpt = '<p>' . $the_excerpt . '</p>';
		return $the_excerpt;
	}


	// Use HTML5 FIGURE and FIGCAPTION for images and captions
	function im_cleaner_captions( $output, $attr, $content ) {
		if ( is_feed() )
			return $output;

		$defaults = array(
			'id' => '',
			'align' => 'alignnone',
			'width' => '',
			'caption' => ''
		);

		$attr = shortcode_atts( $defaults, $attr );

		if ( 1 > $attr['width'] || empty( $attr['caption'] ) )
			return $content;

		$attributes = ( !empty( $attr['id'] ) ? ' id="' . esc_attr( $attr['id'] ) . '"' : '' );
		$attributes .= ' class="wp-caption ' . esc_attr( $attr['align'] ) . '"';

		$output = '<figure' . $attributes .'>';
		$output .= do_shortcode( $content );
		$output .= '<figcaption class="wp-caption-text"><p>' . $attr['caption'] . '</p></figcaption>';
		$output .= '</figure>';

		return $output;
	}
	add_filter( 'img_caption_shortcode', 'im_cleaner_captions', 10, 3 );


// ++++++++++++++++ COMMENTS ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	// Disable comments on media files
	function filter_media_comment_status( $open, $post_id ) {
		$post = get_post( $post_id );
		if( $post->post_type == 'attachment' ) {
			return false;
		}
		return $open;
	}
	add_filter( 'comments_open', 'filter_media_comment_status', 10 , 2 );


	// Close comments globally
	function im_closeCommentsGlobaly($data) { return false; }
	add_filter('comments_number', 'im_closeCommentsGlobaly');
	add_filter('comments_open', 'im_closeCommentsGlobaly');


// ++++++++++++++++ LOAD THEME OPTIONS ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ //

	// Load theme options
	require_once ( get_template_directory() . '/_inc/options.php' );

// ====== END ====== //

}

add_action( 'after_setup_theme', 'im_setup' );

?>