diff --git a/theme/afterburner/config.php b/theme/afterburner/config.php
index fe0673f9165..7fdddb456c3 100644
--- a/theme/afterburner/config.php
+++ b/theme/afterburner/config.php
@@ -1,12 +1,34 @@
 <?php
+// This file is part of Moodle - http://moodle.org/
+//
+// Moodle is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// Moodle is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Moodle.  If not, see <http://www.gnu.org/licenses/>.
+
+/**
+ * Afterburner theme configuration.
+ *
+ * @package    theme_afterburner
+ * @copyright  2011 Mary Evans
+ * @license    http://www.gnu.org/copyleft/gpl.html GNU GPL v3 or later
+ */
 
 $THEME->name = 'afterburner';
 
 $THEME->parents = array('base');
 
 $THEME->sheets = array(
-    'afterburner_pagelayout',   /** Must come first: page layout **/
-    'afterburner_styles',   /** Must come second: default styles **/
+    'afterburner_pagelayout', // Must come first: page layout.
+    'afterburner_styles', // Must come second: default styles.
     'afterburner_menu',
     'afterburner_blocks',
     'afterburner_mod',
@@ -19,7 +41,7 @@ $THEME->sheets = array(
 );
 
 $THEME->parents_exclude_sheets = array(
-    'base'=>array(
+    'base' => array(
         'pagelayout',
         'dock'
     ),
@@ -27,18 +49,18 @@ $THEME->parents_exclude_sheets = array(
 $THEME->editor_sheets = array('editor');
 
 $THEME->layouts = array(
-    // Most backwards compatible layout without the blocks - this is the layout used by default
+    // Most backwards compatible layout without the blocks - this is the layout used by default.
     'base' => array(
         'file' => 'default.php',
         'regions' => array(),
     ),
-    // Standard layout with blocks, this is recommended for most pages with default information
+    // Standard layout with blocks, this is recommended for most pages with default information.
     'standard' => array(
         'file' => 'default.php',
         'regions' => array('side-pre', 'side-post'),
         'defaultregion' => 'side-pre',
     ),
-    // Main course page
+    // Main course page.
     'course' => array(
         'file' => 'default.php',
         'regions' => array('side-pre', 'side-post'),
@@ -50,7 +72,7 @@ $THEME->layouts = array(
         'regions' => array('side-pre', 'side-post'),
         'defaultregion' => 'side-pre',
     ),
-    // part of course, typical for modules - default page layout if $cm specified in require_login()
+    // part of course, typical for modules - default page layout if $cm specified in require_login().
     'incourse' => array(
         'file' => 'default.php',
         'regions' => array('side-pre', 'side-post'),
@@ -69,14 +91,14 @@ $THEME->layouts = array(
         'regions' => array('side-pre'),
         'defaultregion' => 'side-pre',
     ),
-    // My dashboard page
+    // My dashboard page.
     'mydashboard' => array(
         'file' => 'default.php',
         'regions' => array('side-post'),
         'defaultregion' => 'side-post',
         'options' => array('langmenu'=>true),
     ),
-    // My public page
+    // My public page.
     'mypublic' => array(
         'file' => 'default.php',
         'regions' => array('side-pre'),
@@ -100,7 +122,7 @@ $THEME->layouts = array(
         'regions' => array(),
         'options' => array('nofooter'=>true, 'nocoursefooter'=>true),
     ),
-    // Embedded pages, like iframe/object embeded in moodleform - it needs as much space as possible
+    // Embedded pages, like iframe/object embeded in moodleform - it needs as much space as possible.
     'embedded' => array(
         'file' => 'embedded.php',
         'regions' => array()
diff --git a/theme/afterburner/db/upgrade.php b/theme/afterburner/db/upgrade.php
index 4900a2c4446..6377625ac54 100644
--- a/theme/afterburner/db/upgrade.php
+++ b/theme/afterburner/db/upgrade.php
@@ -22,6 +22,12 @@
  * @license    http://www.gnu.org/copyleft/gpl.html GNU GPL v3 or later
  */
 
+/**
+ * Upgrade steps for the Afterburner theme.
+ *
+ * @param int $oldversion
+ * @return bool
+ */
 function xmldb_theme_afterburner_upgrade($oldversion) {
     global $CFG, $DB, $OUTPUT;
 
diff --git a/theme/afterburner/lang/en/theme_afterburner.php b/theme/afterburner/lang/en/theme_afterburner.php
index 1f140a32277..462d1d81834 100644
--- a/theme/afterburner/lang/en/theme_afterburner.php
+++ b/theme/afterburner/lang/en/theme_afterburner.php
@@ -1,5 +1,4 @@
 <?php
-
 // This file is part of Moodle - http://moodle.org/
 //
 // Moodle is free software: you can redistribute it and/or modify
diff --git a/theme/afterburner/layout/default.php b/theme/afterburner/layout/default.php
index 6c94529a825..47372aaa523 100644
--- a/theme/afterburner/layout/default.php
+++ b/theme/afterburner/layout/default.php
@@ -1,4 +1,26 @@
 <?php
+// This file is part of Moodle - http://moodle.org/
+//
+// Moodle is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// Moodle is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Moodle.  If not, see <http://www.gnu.org/licenses/>.
+
+/**
+ * The default layout for the afterburner theme.
+ *
+ * @package    theme_afterburner
+ * @copyright  2011 Mary Evans
+ * @license    http://www.gnu.org/copyleft/gpl.html GNU GPL v3 or later
+ */
 
 $hasheading = ($PAGE->heading);
 $hasnavbar = (empty($PAGE->layout_options['nonavbar']) && $PAGE->has_navbar());
diff --git a/theme/afterburner/layout/embedded.php b/theme/afterburner/layout/embedded.php
index 9d39e027491..31721284e83 100644
--- a/theme/afterburner/layout/embedded.php
+++ b/theme/afterburner/layout/embedded.php
@@ -1,4 +1,30 @@
-<?php echo $OUTPUT->doctype() ?>
+<?php
+// This file is part of Moodle - http://moodle.org/
+//
+// Moodle is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// Moodle is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Moodle.  If not, see <http://www.gnu.org/licenses/>.
+
+/**
+ * The embedded layout.
+ *
+ * This layout is used for content that is embedded within an existing Moodle page.
+ *
+ * @package    theme_afterburner
+ * @copyright  2011 Mary Evans
+ * @license    http://www.gnu.org/copyleft/gpl.html GNU GPL v3 or later
+ */
+
+echo $OUTPUT->doctype() ?>
 <html <?php echo $OUTPUT->htmlattributes() ?>>
 <head>
     <title><?php echo $PAGE->title ?></title>
diff --git a/theme/afterburner/lib.php b/theme/afterburner/lib.php
index 7d2a1406bf4..aaddd0020ca 100644
--- a/theme/afterburner/lib.php
+++ b/theme/afterburner/lib.php
@@ -1,12 +1,44 @@
 <?php
+// This file is part of Moodle - http://moodle.org/
+//
+// Moodle is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// Moodle is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Moodle.  If not, see <http://www.gnu.org/licenses/>.
 
+/**
+ * This file contains functions specific to the needs of the afterburner theme.
+ *
+ * @package    theme_afterburner
+ * @copyright  2011 Mary Evans
+ * @license    http://www.gnu.org/copyleft/gpl.html GNU GPL v3 or later
+ */
+
+/**
+ * Processes CSS for the afterburner theme before it is cached and delivered.
+ *
+ * This function performs any customisations on the CSS that this theme requires.
+ * This includes setting the theme logo, and including any custom CSS.
+ *
+ * @param string $css The raw CSS.
+ * @param theme_config $theme
+ * @return string The now processed CSS.
+ */
 function afterburner_process_css($css, $theme) {
 
-    // Set the background image for the logo
+    // Set the background image for the logo.
     $logo = $theme->setting_file_url('logo', 'logo');
     $css = afterburner_set_logo($css, $logo, $theme);
 
-    // Set custom CSS
+    // Set custom CSS.
     if (!empty($theme->settings->customcss)) {
         $customcss = $theme->settings->customcss;
     } else {
@@ -17,11 +49,19 @@ function afterburner_process_css($css, $theme) {
     return $css;
 }
 
+/**
+ * Adds the set logo to the CSS before it is cached and delivered.
+ *
+ * @param string $css
+ * @param string $logo
+ * @param theme_config $theme
+ * @return string
+ */
 function afterburner_set_logo($css, $logo, $theme) {
     $tag = '[[setting:logo]]';
     $replacement = $logo;
     if (is_null($replacement)) {
-        $replacement = $theme->pix_url('images/logo','theme');
+        $replacement = $theme->pix_url('images/logo', 'theme');
     }
 
     $css = str_replace($tag, $replacement, $css);
@@ -29,6 +69,12 @@ function afterburner_set_logo($css, $logo, $theme) {
     return $css;
 }
 
+/**
+ * Adds any custom CSS the admin has set to the CSS file before it is cached and delivered.
+ * @param string $css
+ * @param string $customcss
+ * @return string
+ */
 function afterburner_set_customcss($css, $customcss) {
     $tag = '[[setting:customcss]]';
     $replacement = $customcss;
@@ -41,6 +87,18 @@ function afterburner_set_customcss($css, $customcss) {
     return $css;
 }
 
+/**
+ * Serves any theme associated files when they are requested.
+ *
+ * @param stdClass $course
+ * @param cm_info $cm
+ * @param context $context
+ * @param string $filearea
+ * @param array $args
+ * @param bool $forcedownload
+ * @param array $options
+ * @return bool
+ */
 function theme_afterburner_pluginfile($course, $cm, $context, $filearea, $args, $forcedownload, array $options = array()) {
     if ($context->contextlevel == CONTEXT_SYSTEM and $filearea === 'logo') {
         $theme = theme_config::load('afterburner');
diff --git a/theme/afterburner/renderers.php b/theme/afterburner/renderers.php
index 70fdebeb312..69659276ecd 100644
--- a/theme/afterburner/renderers.php
+++ b/theme/afterburner/renderers.php
@@ -1,5 +1,36 @@
 <?php
+// This file is part of Moodle - http://moodle.org/
+//
+// Moodle is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// Moodle is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Moodle.  If not, see <http://www.gnu.org/licenses/>.
 
+/**
+ * Afterburner overridden renderers.
+ *
+ * This file contains renderers that have been overridden by the afterburner theme.
+ *
+ * @package    theme_afterburner
+ * @copyright  2011 Mary Evans
+ * @license    http://www.gnu.org/copyleft/gpl.html GNU GPL v3 or later
+ */
+
+/**
+ * Overridden core_renderer.
+ *
+ * @package    theme_afterburner
+ * @copyright  2011 Mary Evans
+ * @license    http://www.gnu.org/copyleft/gpl.html GNU GPL v3 or later
+ */
 class theme_afterburner_core_renderer extends core_renderer {
 
     /**
@@ -13,12 +44,12 @@ class theme_afterburner_core_renderer extends core_renderer {
      */
     protected function render_custom_menu(custom_menu $menu) {
 
-        // If the menu has no children return an empty string
+        // If the menu has no children return an empty string.
         if (!$menu->has_children()) {
             return '';
         }
 
-        // Add a login or logout link
+        // Add a login or logout link.
         if (isloggedin()) {
             $branchlabel = get_string('logout');
             $branchurl   = new moodle_url('/login/logout.php');
@@ -28,15 +59,15 @@ class theme_afterburner_core_renderer extends core_renderer {
         }
         $branch = $menu->add($branchlabel, $branchurl, $branchlabel, -1);
 
-        // Initialise this custom menu
-        $content = html_writer::start_tag('ul', array('class'=>'dropdown dropdown-horizontal'));
-        // Render each child
+        // Initialise this custom menu.
+        $content = html_writer::start_tag('ul', array('class' => 'dropdown dropdown-horizontal'));
+        // Render each child.
         foreach ($menu->get_children() as $item) {
             $content .= $this->render_custom_menu_item($item);
         }
-        // Close the open tags
+        // Close the open tags.
         $content .= html_writer::end_tag('ul');
-        // Return the custom menu
+        // Return the custom menu.
         return $content;
     }
 
@@ -53,19 +84,19 @@ class theme_afterburner_core_renderer extends core_renderer {
      * @return string
      */
     protected function render_custom_menu_item(custom_menu_item $menunode) {
-        // Required to ensure we get unique trackable id's
+        // Required to ensure we get unique trackable id's.
         static $submenucount = 0;
         $content = html_writer::start_tag('li');
         if ($menunode->has_children()) {
-            // If the child has menus render it as a sub menu
+            // If the child has menus render it as a sub menu.
             $submenucount++;
             if ($menunode->get_url() !== null) {
                 $url = $menunode->get_url();
             } else {
                 $url = '#cm_submenu_'.$submenucount;
             }
-            $content .= html_writer::start_tag('span', array('class'=>'customitem'));
-            $content .= html_writer::link($url, $menunode->get_text(), array('title'=>$menunode->get_title()));
+            $content .= html_writer::start_tag('span', array('class' => 'customitem'));
+            $content .= html_writer::link($url, $menunode->get_text(), array('title' => $menunode->get_title()));
             $content .= html_writer::end_tag('span');
             $content .= html_writer::start_tag('ul');
             foreach ($menunode->get_children() as $menunode) {
@@ -73,17 +104,17 @@ class theme_afterburner_core_renderer extends core_renderer {
             }
             $content .= html_writer::end_tag('ul');
         } else {
-            // The node doesn't have children so produce a final menuitem
+            // The node doesn't have children so produce a final menuitem.
 
             if ($menunode->get_url() !== null) {
                 $url = $menunode->get_url();
             } else {
                 $url = '#';
             }
-            $content .= html_writer::link($url, $menunode->get_text(), array('title'=>$menunode->get_title()));
+            $content .= html_writer::link($url, $menunode->get_text(), array('title' => $menunode->get_title()));
         }
         $content .= html_writer::end_tag('li');
-        // Return the sub menu
+        // Return the sub menu.
         return $content;
     }
 
@@ -98,16 +129,16 @@ class theme_afterburner_core_renderer extends core_renderer {
         $title = $item->get_title();
         if ($item->icon instanceof renderable && !$item->hideicon) {
             $icon = $this->render($item->icon);
-            $content = $icon.$content; // use CSS for spacing of icons
+            $content = $icon.$content; // Use CSS for spacing of icons.
         }
         if ($item->helpbutton !== null) {
-            $content = trim($item->helpbutton).html_writer::tag('span', $content, array('class'=>'clearhelpbutton'));
+            $content = trim($item->helpbutton).html_writer::tag('span', $content, array('class' => 'clearhelpbutton'));
         }
         if ($content === '') {
             return '';
         }
         if ($item->action instanceof action_link) {
-            //adds class dimmed to hidden courses and categories
+            // Adds class dimmed to hidden courses and categories.
             $link = $item->action;
             if ($item->hidden) {
                 $link->add_class('dimmed');
diff --git a/theme/afterburner/settings.php b/theme/afterburner/settings.php
index f96867b60ee..a0cf68e38d4 100644
--- a/theme/afterburner/settings.php
+++ b/theme/afterburner/settings.php
@@ -1,29 +1,51 @@
 <?php
+// This file is part of Moodle - http://moodle.org/
+//
+// Moodle is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// Moodle is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Moodle.  If not, see <http://www.gnu.org/licenses/>.
+
+/**
+ * Afterburner theme settings.
+ *
+ * @package    theme_afterburner
+ * @copyright  2011 Mary Evans
+ * @license    http://www.gnu.org/copyleft/gpl.html GNU GPL v3 or later
+ */
 
 defined('MOODLE_INTERNAL') || die;
 
 if ($ADMIN->fulltree) {
 
-    // Logo file setting
+    // Logo file setting.
     $name = 'theme_afterburner/logo';
-    $title = get_string('logo','theme_afterburner');
+    $title = get_string('logo', 'theme_afterburner');
     $description = get_string('logodesc', 'theme_afterburner');
     $setting = new admin_setting_configstoredfile($name, $title, $description, 'logo');
     $setting->set_updatedcallback('theme_reset_all_caches');
     $settings->add($setting);
 
-    // Foot note setting
+    // Foot note setting.
     $name = 'theme_afterburner/footnote';
-    $title = get_string('footnote','theme_afterburner');
+    $title = get_string('footnote', 'theme_afterburner');
     $description = get_string('footnotedesc', 'theme_afterburner');
     $default = '';
     $setting = new admin_setting_confightmleditor($name, $title, $description, $default);
     $setting->set_updatedcallback('theme_reset_all_caches');
     $settings->add($setting);
 
-    // Custom CSS file
+    // Custom CSS file.
     $name = 'theme_afterburner/customcss';
-    $title = get_string('customcss','theme_afterburner');
+    $title = get_string('customcss', 'theme_afterburner');
     $description = get_string('customcssdesc', 'theme_afterburner');
     $default = '';
     $setting = new admin_setting_configtextarea($name, $title, $description, $default);
diff --git a/theme/afterburner/version.php b/theme/afterburner/version.php
index be85bc00bf3..f31fe5665d4 100644
--- a/theme/afterburner/version.php
+++ b/theme/afterburner/version.php
@@ -26,7 +26,7 @@ defined('MOODLE_INTERNAL') || die;
 
 $plugin->version   = 2013110500; // The current module version (Date: YYYYMMDDXX)
 $plugin->requires  = 2013110500; // Requires this Moodle version
-$plugin->component = 'theme_afterburner'; // Full name of the plugin (used for diagnostics)
+$plugin->component = 'theme_afterburner'; // Full name of the plugin (used for diagnostics).
 $plugin->dependencies = array(
     'theme_base'  => 2013110500,
 );