diff --git a/doc/usage.md b/doc/usage.md
index a952236..a41d0b6 100755
--- a/doc/usage.md
+++ b/doc/usage.md
@@ -5,7 +5,7 @@ table of contents](TOC.md)
 
 The HTML, CSS and JavaScript in Roots comes from a combination of HTML5 Boilerplate and Twitter Bootstrap.
 
-* [HTML5 Boilerplate documentation](https://github.com/h5bp/html5-boilerplate/blob/master/doc/README.md)
+* [HTML5 Boilerplate documentation](https://github.com/h5bp/html5-boilerplate/blob/master/README.md)
 * [Twitter Bootstrap documentation](http://twitter.github.com/bootstrap/getting-started.html)
 
 ## Basic structure
diff --git a/functions.php b/functions.php
index 62e8841..fef4745 100644
--- a/functions.php
+++ b/functions.php
@@ -1,10 +1,7 @@
 <?php
 /**
- * Required by WordPress.
- *
- * Keep this file clean and only use it for requires.
+ * Roots includes
  */
-
 require_once locate_template('/lib/utils.php');           // Utility functions
 require_once locate_template('/lib/init.php');            // Initial theme setup and constants
 require_once locate_template('/lib/sidebar.php');         // Sidebar class
diff --git a/lib/activation.php b/lib/activation.php
index 3f6a481..ce8add8 100644
--- a/lib/activation.php
+++ b/lib/activation.php
@@ -1,5 +1,7 @@
 <?php
-
+/**
+ * Theme activation
+ */
 if (is_admin() && isset($_GET['activated']) && 'themes.php' == $GLOBALS['pagenow']) {
   wp_redirect(admin_url('themes.php?page=theme_activation_options'));
   exit;
diff --git a/lib/cleanup.php b/lib/cleanup.php
index 45a48ea..7c49a0d 100644
--- a/lib/cleanup.php
+++ b/lib/cleanup.php
@@ -1,5 +1,4 @@
 <?php
-
 /**
  * Clean up wp_head()
  *
@@ -43,7 +42,6 @@ function roots_rel_canonical() {
   $link = get_permalink($id);
   echo "\t<link rel=\"canonical\" href=\"$link\">\n";
 }
-
 add_action('init', 'roots_head_cleanup');
 
 /**
@@ -80,7 +78,6 @@ function roots_language_attributes() {
 
   return $output;
 }
-
 add_filter('language_attributes', 'roots_language_attributes');
 
 /**
@@ -92,7 +89,6 @@ function roots_clean_style_tag($input) {
   $media = $matches[3][0] === 'print' ? ' media="print"' : '';
   return '<link rel="stylesheet" href="' . $matches[2][0] . '"' . $media . '>' . "\n";
 }
-
 add_filter('style_loader_tag', 'roots_clean_style_tag');
 
 /**
@@ -114,7 +110,6 @@ function roots_body_class($classes) {
 
   return $classes;
 }
-
 add_filter('body_class', 'roots_body_class');
 
 /**
@@ -129,6 +124,11 @@ add_filter('body_class', 'roots_body_class');
  * @author Scott Walkinshaw <scott.walkinshaw@gmail.com>
  */
 function roots_root_relative_url($input) {
+  // fix for site_url != home_url()
+  if(!is_admin() && site_url() != home_url()) {
+  	$input = str_replace(site_url(), "", $input);
+  }
+  
   $output = preg_replace_callback(
     '!(https?://[^/|"]+)([^"]+)?!',
     create_function(
@@ -142,22 +142,12 @@ function roots_root_relative_url($input) {
     ),
     $input
   );
-
-  return $output;
-}
-
-/**
- * Terrible workaround to remove the duplicate subfolder in the src of <script> and <link> tags
- * Example: /subfolder/subfolder/css/style.css
- */
-function roots_fix_duplicate_subfolder_urls($input) {
-  $output = roots_root_relative_url($input);
-  preg_match_all('!([^/]+)/([^/]+)!', $output, $matches);
-
-  if (isset($matches[1][0]) && isset($matches[2][0])) {
-    if ($matches[1][0] === $matches[2][0]) {
-      $output = substr($output, strlen($matches[1][0]) + 1);
-    }
+  
+  // detect and correct for subdir installs
+  if($subdir = parse_url(home_url(), PHP_URL_PATH)) {
+  	if(substr($output, 0, strlen($subdir)) == (substr($output, strlen($subdir), strlen($subdir)))) {
+  		$output = substr($output, strlen($subdir));
+  	}
   }
 
   return $output;
@@ -186,13 +176,12 @@ if (roots_enable_root_relative_urls()) {
     'day_link',
     'year_link',
     'tag_link',
-    'the_author_posts_link'
+    'the_author_posts_link',
+  	'script_loader_src',
+  	'style_loader_src'
   );
 
   add_filters($root_rel_filters, 'roots_root_relative_url');
-
-  add_filter('script_loader_src', 'roots_fix_duplicate_subfolder_urls');
-  add_filter('style_loader_src', 'roots_fix_duplicate_subfolder_urls');
 }
 
 /**
@@ -204,7 +193,6 @@ if (roots_enable_root_relative_urls()) {
 function roots_embed_wrap($cache, $url, $attr = '', $post_ID = '') {
   return '<div class="entry-content-asset">' . $cache . '</div>';
 }
-
 add_filter('embed_oembed_html', 'roots_embed_wrap', 10, 4);
 add_filter('embed_googlevideo', 'roots_embed_wrap', 10, 2);
 
@@ -216,7 +204,6 @@ function roots_attachment_link_class($html) {
   $html = str_replace('<a', '<a class="thumbnail"', $html);
   return $html;
 }
-
 add_filter('wp_get_attachment_link', 'roots_attachment_link_class', 10, 1);
 
 /**
@@ -256,7 +243,6 @@ function roots_caption($output, $attr, $content) {
 
   return $output;
 }
-
 add_filter('img_caption_shortcode', 'roots_caption', 10, 3);
 
 /**
@@ -353,7 +339,6 @@ function roots_gallery($attr) {
 
   return $output;
 }
-
 if (current_theme_supports('bootstrap-gallery')) {
   remove_shortcode('gallery');
   add_shortcode('gallery', 'roots_gallery');
@@ -370,7 +355,6 @@ function roots_remove_dashboard_widgets() {
   remove_meta_box('dashboard_primary', 'dashboard', 'normal');
   remove_meta_box('dashboard_secondary', 'dashboard', 'normal');
 }
-
 add_action('admin_init', 'roots_remove_dashboard_widgets');
 
 /**
@@ -383,7 +367,6 @@ function roots_excerpt_length($length) {
 function roots_excerpt_more($more) {
   return ' &hellip; <a href="' . get_permalink() . '">' . __('Continued', 'roots') . '</a>';
 }
-
 add_filter('excerpt_length', 'roots_excerpt_length');
 add_filter('excerpt_more', 'roots_excerpt_more');
 
@@ -393,7 +376,6 @@ add_filter('excerpt_more', 'roots_excerpt_more');
 function roots_remove_self_closing_tags($input) {
   return str_replace(' />', '>', $input);
 }
-
 add_filter('get_avatar',          'roots_remove_self_closing_tags'); // <img />
 add_filter('comment_id_fields',   'roots_remove_self_closing_tags'); // <input />
 add_filter('post_thumbnail_html', 'roots_remove_self_closing_tags'); // <img />
@@ -403,10 +385,8 @@ add_filter('post_thumbnail_html', 'roots_remove_self_closing_tags'); // <img />
  */
 function roots_remove_default_description($bloginfo) {
   $default_tagline = 'Just another WordPress site';
-
   return ($bloginfo === $default_tagline) ? '' : $bloginfo;
 }
-
 add_filter('get_bloginfo_rss', 'roots_remove_default_description');
 
 /**
@@ -423,7 +403,6 @@ function roots_change_mce_options($options) {
 
   return $options;
 }
-
 add_filter('tiny_mce_before_init', 'roots_change_mce_options');
 
 /**
@@ -463,7 +442,6 @@ function roots_widget_first_last_classes($params) {
 
   return $params;
 }
-
 add_filter('dynamic_sidebar_params', 'roots_widget_first_last_classes');
 
 /**
@@ -483,7 +461,6 @@ function roots_nice_search_redirect() {
     exit();
   }
 }
-
 if (current_theme_supports('nice-search')) {
   add_action('template_redirect', 'roots_nice_search_redirect');
 }
@@ -501,7 +478,6 @@ function roots_request_filter($query_vars) {
 
   return $query_vars;
 }
-
 add_filter('request', 'roots_request_filter');
 
 /**
@@ -512,5 +488,4 @@ function roots_get_search_form($argument) {
     locate_template('/templates/searchform.php', true, false);
   }
 }
-
 add_filter('get_search_form', 'roots_get_search_form');
diff --git a/lib/comments.php b/lib/comments.php
index 62f4c3e..5131fe2 100644
--- a/lib/comments.php
+++ b/lib/comments.php
@@ -1,11 +1,4 @@
 <?php
-
-function roots_get_avatar($avatar) {
-  $avatar = str_replace("class='avatar", "class='avatar pull-left media-object", $avatar);
-  return $avatar;
-}
-add_filter('get_avatar', 'roots_get_avatar');
-
 /**
  * Use Bootstrap's media object for listing comments
  *
@@ -61,3 +54,9 @@ class Roots_Walker_Comment extends Walker_Comment {
     echo "</li>\n";
   }
 }
+
+function roots_get_avatar($avatar) {
+  $avatar = str_replace("class='avatar", "class='avatar pull-left media-object", $avatar);
+  return $avatar;
+}
+add_filter('get_avatar', 'roots_get_avatar');
diff --git a/lib/config.php b/lib/config.php
index ae11d9b..e951476 100644
--- a/lib/config.php
+++ b/lib/config.php
@@ -1,5 +1,4 @@
 <?php
-
 /**
  * Enable theme features
  */
diff --git a/lib/custom.php b/lib/custom.php
index c63de83..a7a52fb 100644
--- a/lib/custom.php
+++ b/lib/custom.php
@@ -1,3 +1,4 @@
 <?php
-
-// Custom functions
+/**
+ * Custom functions
+ */
diff --git a/lib/htaccess.php b/lib/htaccess.php
index 98701ce..57923a8 100644
--- a/lib/htaccess.php
+++ b/lib/htaccess.php
@@ -2,8 +2,6 @@
 /**
  * Add HTML5 Boilerplate's .htaccess via WordPress
  */
-
-// Add the contents of h5bp-htaccess into .htaccess
 function roots_add_h5bp_htaccess($content) {
   global $wp_rewrite;
   $home_path = function_exists('get_home_path') ? get_home_path() : ABSPATH;
diff --git a/lib/init.php b/lib/init.php
index 3314679..9fa9954 100644
--- a/lib/init.php
+++ b/lib/init.php
@@ -2,9 +2,7 @@
 /**
  * Roots initial setup and constants
  */
-
 function roots_setup() {
-
   // Make theme available for translation
   load_theme_textdomain('roots', get_template_directory() . '/lang');
 
@@ -23,9 +21,7 @@ function roots_setup() {
 
   // Tell the TinyMCE editor to use a custom stylesheet
   add_editor_style('/assets/css/editor-style.css');
-
 }
-
 add_action('after_setup_theme', 'roots_setup');
 
 // Backwards compatibility for older than PHP 5.3.0
diff --git a/lib/nav.php b/lib/nav.php
index a53b05f..7e5b548 100644
--- a/lib/nav.php
+++ b/lib/nav.php
@@ -1,5 +1,4 @@
 <?php
-
 /**
  * Cleaner walker for wp_nav_menu()
  *
@@ -29,11 +28,11 @@ class Roots_Nav_Walker extends Walker_Nav_Menu {
       $item_html = str_replace('</a>', ' <b class="caret"></b></a>', $item_html);
     }
     elseif (stristr($item_html, 'li class="divider')) {
-      $item_html = preg_replace('/<a[^>]*>.*?<\/a>/iU', '', $item_html);    
+      $item_html = preg_replace('/<a[^>]*>.*?<\/a>/iU', '', $item_html);
     }
     elseif (stristr($item_html, 'li class="nav-header')) {
       $item_html = preg_replace('/<a[^>]*>(.*)<\/a>/iU', '$1', $item_html);
-    }   
+    }
 
     $output .= $item_html;
   }
@@ -68,7 +67,6 @@ function roots_nav_menu_css_class($classes, $item) {
 
   return array_filter($classes, 'is_element_empty');
 }
-
 add_filter('nav_menu_css_class', 'roots_nav_menu_css_class', 10, 2);
 add_filter('nav_menu_item_id', '__return_null');
 
@@ -95,7 +93,4 @@ function roots_nav_menu_args($args = '') {
 
   return array_merge($args, $roots_nav_menu_args);
 }
-
 add_filter('wp_nav_menu_args', 'roots_nav_menu_args');
-
-
diff --git a/lib/rewrites.php b/lib/rewrites.php
index 72286eb..e2db26d 100644
--- a/lib/rewrites.php
+++ b/lib/rewrites.php
@@ -15,7 +15,6 @@
  *
  * @link https://github.com/retlehs/roots/blob/master/doc/rewrites.md
  */
-
 function roots_add_rewrites($content) {
   global $wp_rewrite;
   $roots_new_non_wp_rules = array(
diff --git a/lib/scripts.php b/lib/scripts.php
index 34a2082..1c32d97 100644
--- a/lib/scripts.php
+++ b/lib/scripts.php
@@ -1,6 +1,6 @@
 <?php
 /**
- * Scripts and stylesheets
+ * Enqueue scripts and stylesheets
  *
  * Enqueue stylesheets in the following order:
  * 1. /theme/assets/css/main.min.css
@@ -10,7 +10,6 @@
  * 2. /theme/assets/js/vendor/modernizr-2.6.2.min.js
  * 3. /theme/assets/js/scripts.min.js
  */
-
 function roots_scripts() {
   wp_enqueue_style('roots_main', get_template_directory_uri() . '/assets/css/main.min.css', false, '99a8db779c85fab09c1780951893470f');
 
@@ -37,7 +36,6 @@ function roots_scripts() {
   wp_enqueue_script('jquery');
   wp_enqueue_script('roots_scripts');
 }
-
 add_action('wp_enqueue_scripts', 'roots_scripts', 100);
 
 // http://wordpress.stackexchange.com/a/12450
@@ -55,7 +53,6 @@ function roots_jquery_local_fallback($src, $handle) {
 
   return $src;
 }
-
 if (!is_admin()) {
   add_filter('script_loader_src', 'roots_jquery_local_fallback', 10, 2);
 }
@@ -68,7 +65,6 @@ function roots_google_analytics() { ?>
     s.parentNode.insertBefore(g,s)}(document,'script'));
 </script>
 <?php }
-
 if (GOOGLE_ANALYTICS_ID) {
   add_action('wp_footer', 'roots_google_analytics', 20);
 }
diff --git a/lib/sidebar.php b/lib/sidebar.php
index 3d783ee..8bff99c 100644
--- a/lib/sidebar.php
+++ b/lib/sidebar.php
@@ -40,4 +40,3 @@ class Roots_Sidebar {
     return is_page_template($page_template);
   }
 }
-?>
diff --git a/lib/utils.php b/lib/utils.php
index cf688de..538ca41 100644
--- a/lib/utils.php
+++ b/lib/utils.php
@@ -1,7 +1,6 @@
 <?php
-
 /**
- * Theme Wrapper
+ * Theme wrapper
  *
  * @link http://scribu.net/wordpress/theme-wrappers.html
  */
@@ -48,10 +47,8 @@ class Roots_Wrapping {
     return locate_template($templates);
   }
 }
-
 add_filter('template_include', array('Roots_Wrapping', 'wrap'), 99);
 
-
 /**
  * Page titles
  */
@@ -98,10 +95,11 @@ function roots_htaccess_writable() {
     }
   }
 }
-
 add_action('admin_init', 'roots_htaccess_writable');
 
-// returns WordPress subdirectory if applicable
+/**
+ * Return WordPress subdirectory if applicable
+ */
 function wp_base_dir() {
   preg_match('!(https?://[^/|"]+)([^"]+)?!', site_url(), $matches);
   if (count($matches) === 3) {
@@ -111,7 +109,9 @@ function wp_base_dir() {
   }
 }
 
-// opposite of built in WP functions for trailing slashes
+/**
+ * Opposite of built in WP functions for trailing slashes
+ */
 function leadingslashit($string) {
   return '/' . unleadingslashit($string);
 }
diff --git a/lib/widgets.php b/lib/widgets.php
index ec654dd..fd067d1 100644
--- a/lib/widgets.php
+++ b/lib/widgets.php
@@ -1,7 +1,9 @@
 <?php
-
+/**
+ * Register sidebars and widgets
+ */
 function roots_widgets_init() {
-  // Register widgetized areas
+  // Sidebars
   register_sidebar(array(
     'name'          => __('Primary Sidebar', 'roots'),
     'id'            => 'sidebar-primary',
@@ -20,12 +22,14 @@ function roots_widgets_init() {
     'after_title'   => '</h3>',
   ));
 
-  // Register widgets
+  // Widgets
   register_widget('Roots_Vcard_Widget');
 }
 add_action('widgets_init', 'roots_widgets_init');
 
-// Example vCard widget
+/**
+ * Example vCard widget
+ */
 class Roots_Vcard_Widget extends WP_Widget {
   private $fields = array(
     'title'          => 'Title (optional)',