diff --git a/modules/system/classes/PluginManager.php b/modules/system/classes/PluginManager.php
index 4d8894c92..26e38c10d 100644
--- a/modules/system/classes/PluginManager.php
+++ b/modules/system/classes/PluginManager.php
@@ -3,15 +3,15 @@
 use Db;
 use App;
 use Str;
+use Log;
 use File;
 use Lang;
-use Log;
 use View;
 use Config;
 use Schema;
+use SystemException;
 use RecursiveIteratorIterator;
 use RecursiveDirectoryIterator;
-use SystemException;
 
 /**
  * Plugin manager
@@ -29,7 +29,7 @@ class PluginManager
     protected $app;
 
     /**
-     * Container object used for storing plugin information objects.
+     * @var array Container array used for storing plugin information objects.
      */
     protected $plugins;
 
@@ -44,22 +44,22 @@ class PluginManager
     protected $normalizedMap = [];
 
     /**
-     * @var bool Check if all plugins have had the register() method called.
+     * @var bool Flag to indicate that all plugins have had the register() method called by registerAll() being called on this class.
      */
     protected $registered = false;
 
     /**
-     * @var bool Check if all plugins have had the boot() method called.
+     * @var bool Flag to indicate that all plugins have had the boot() method called by bootAll() being called on this class.
      */
     protected $booted = false;
 
     /**
-     * @var string Path to the disarm file.
+     * @var string Path to the JSON encoded file containing the disabled plugins.
      */
     protected $metaFile;
 
     /**
-     * @var array Collection of disabled plugins
+     * @var array Array of disabled plugins
      */
     protected $disabledPlugins = [];
 
@@ -69,7 +69,7 @@ class PluginManager
     protected $registrationMethodCache = [];
 
     /**
-     * @var boolean Prevent all plugins from registering or booting
+     * @var bool Prevent all plugins from registering or booting
      */
     public static $noInit = false;
 
@@ -99,7 +99,8 @@ class PluginManager
     }
 
     /**
-     * Finds all available plugins and loads them in to the $plugins array.
+     * Finds all available plugins and loads them in to the $this->plugins array.
+     *
      * @return array
      */
     public function loadPlugins()
@@ -119,15 +120,16 @@ class PluginManager
     }
 
     /**
-     * Loads a single plugin in to the manager.
+     * Loads a single plugin into the manager.
+     *
      * @param string $namespace Eg: Acme\Blog
      * @param string $path Eg: plugins_path().'/acme/blog';
      * @return void
      */
     public function loadPlugin($namespace, $path)
     {
-        $className = $namespace.'\Plugin';
-        $classPath = $path.'/Plugin.php';
+        $className = $namespace . '\Plugin';
+        $classPath = $path . '/Plugin.php';
 
         try {
             // Autoloader failed?
@@ -169,6 +171,8 @@ class PluginManager
 
     /**
      * Runs the register() method on all plugins. Can only be called once.
+     *
+     * @param bool $force Defaults to false, if true will force the re-registration of all plugins. Use unregisterAll() instead.
      * @return void
      */
     public function registerAll($force = false)
@@ -185,7 +189,8 @@ class PluginManager
     }
 
     /**
-     * Unregisters all plugins: the negative of registerAll().
+     * Unregisters all plugins: the inverse of registerAll().
+     *
      * @return void
      */
     public function unregisterAll()
@@ -196,8 +201,9 @@ class PluginManager
 
     /**
      * Registers a single plugin object.
-     * @param PluginBase $plugin
-     * @param string $pluginId
+     *
+     * @param PluginBase $plugin The instantiated Plugin object
+     * @param string $pluginId The string identifier for the plugin
      * @return void
      */
     public function registerPlugin($plugin, $pluginId = null)
@@ -210,6 +216,13 @@ class PluginManager
             return;
         }
 
+        /**
+         * Verify that the provided plugin should be registered
+         */
+        if ($plugin->disabled || (self::$noInit && !$plugin->elevated)) {
+            return;
+        }
+
         $pluginPath = $this->getPluginPath($plugin);
         $pluginNamespace = strtolower($pluginId);
 
@@ -221,10 +234,6 @@ class PluginManager
             Lang::addNamespace($pluginNamespace, $langPath);
         }
 
-        if ($plugin->disabled) {
-            return;
-        }
-
         /*
          * Register plugin class autoloaders
          */
@@ -233,9 +242,10 @@ class PluginManager
             ComposerManager::instance()->autoload($pluginPath . '/vendor');
         }
 
-        if (!self::$noInit || $plugin->elevated) {
-            $plugin->register();
-        }
+        /**
+         * Run the plugin's register() method
+         */
+        $plugin->register();
 
         /*
          * Register configuration path
@@ -257,7 +267,7 @@ class PluginManager
          * Add init, if available
          */
         $initFile = $pluginPath . '/init.php';
-        if (!self::$noInit && File::exists($initFile)) {
+        if (File::exists($initFile)) {
             require $initFile;
         }
 
@@ -272,6 +282,9 @@ class PluginManager
 
     /**
      * Runs the boot() method on all plugins. Can only be called once.
+     *
+     * @param bool $force Defaults to false, if true will force the re-booting of all plugins
+     * @return void
      */
     public function bootAll($force = false)
     {
@@ -287,23 +300,25 @@ class PluginManager
     }
 
     /**
-     * Registers a single plugin object.
+     * Boots the provided plugin object.
+     *
      * @param PluginBase $plugin
      * @return void
      */
     public function bootPlugin($plugin)
     {
-        if (!$plugin || $plugin->disabled) {
+        if (!$plugin || $plugin->disabled || (self::$noInit && !$plugin->elevated)) {
             return;
         }
 
-        if (!self::$noInit || $plugin->elevated) {
-            $plugin->boot();
-        }
+        $plugin->boot();
     }
 
     /**
      * Returns the directory path to a plugin
+     *
+     * @param PluginBase|string $id The plugin to get the path for
+     * @return string|null
      */
     public function getPluginPath($id)
     {
@@ -317,8 +332,9 @@ class PluginManager
 
     /**
      * Check if a plugin exists and is enabled.
-     * @param   string $id Plugin identifier, eg: Namespace.PluginName
-     * @return  boolean
+     *
+     * @param string $id Plugin identifier, eg: Namespace.PluginName
+     * @return bool
      */
     public function exists($id)
     {
@@ -326,8 +342,10 @@ class PluginManager
     }
 
     /**
-     * Returns an array with all registered plugins
+     * Returns an array with all enabled plugins
      * The index is the plugin namespace, the value is the plugin information object.
+     *
+     * @return array
      */
     public function getPlugins()
     {
@@ -336,41 +354,42 @@ class PluginManager
 
     /**
      * Returns a plugin registration class based on its namespace (Author\Plugin).
+     *
+     * @param string $namespace
+     * @return PluginBase|null
      */
     public function findByNamespace($namespace)
     {
-        if (!$this->hasPlugin($namespace)) {
-            return null;
-        }
+        $identifier = $this->getIdentifier($namespace);
 
-        $classId = $this->getIdentifier($namespace);
-
-        return $this->plugins[$classId];
+        return $this->plugins[$identifier] ?? null;
     }
 
     /**
      * Returns a plugin registration class based on its identifier (Author.Plugin).
+     *
+     * @param string|PluginBase $identifier
+     * @return PluginBase|null
      */
     public function findByIdentifier($identifier)
     {
         if (!isset($this->plugins[$identifier])) {
-            $identifier = $this->normalizeIdentifier($identifier);
+            $code = $this->getIdentifier($identifier);
+            $identifier = $this->normalizeIdentifier($code);
         }
 
-        if (!isset($this->plugins[$identifier])) {
-            return null;
-        }
-
-        return $this->plugins[$identifier];
+        return $this->plugins[$identifier] ?? null;
     }
 
     /**
      * Checks to see if a plugin has been registered.
+     *
+     * @param string|PluginBase
+     * @return bool
      */
     public function hasPlugin($namespace)
     {
         $classId = $this->getIdentifier($namespace);
-
         $normalized = $this->normalizeIdentifier($classId);
 
         return isset($this->plugins[$normalized]);
@@ -378,6 +397,8 @@ class PluginManager
 
     /**
      * Returns a flat array of vendor plugin namespaces and their paths
+     *
+     * @return array ['Author\Plugin' => 'plugins/author/plugin']
      */
     public function getPluginNamespaces()
     {
@@ -396,6 +417,8 @@ class PluginManager
 
     /**
      * Returns a 2 dimensional array of vendors and their plugins.
+     *
+     * @return array ['vendor' => ['author' => 'plugins/author/plugin']]
      */
     public function getVendorAndPluginNames()
     {
@@ -427,9 +450,10 @@ class PluginManager
     }
 
     /**
-     * Resolves a plugin identifier from a plugin class name or object.
+     * Resolves a plugin identifier (Author.Plugin) from a plugin class name or object.
+     *
      * @param mixed Plugin class name or object
-     * @return string Identifier in format of Vendor.Plugin
+     * @return string Identifier in format of Author.Plugin
      */
     public function getIdentifier($namespace)
     {
@@ -463,7 +487,8 @@ class PluginManager
     }
 
     /**
-     * Spins over every plugin object and collects the results of a method call.
+     * Spins over every plugin object and collects the results of a method call. Results are cached in memory.
+     *
      * @param  string $methodName
      * @return array
      */
@@ -491,6 +516,11 @@ class PluginManager
     // Disability
     //
 
+    /**
+     * Clears the disabled plugins cache file
+     *
+     * @return void
+     */
     public function clearDisabledCache()
     {
         File::delete($this->metaFile);
@@ -498,7 +528,9 @@ class PluginManager
     }
 
     /**
-     * Loads all disables plugins from the meta file.
+     * Loads all disabled plugins from the cached JSON file.
+     *
+     * @return void
      */
     protected function loadDisabled()
     {
@@ -513,8 +545,7 @@ class PluginManager
         if (File::exists($path)) {
             $disabled = json_decode(File::get($path), true) ?: [];
             $this->disabledPlugins = array_merge($this->disabledPlugins, $disabled);
-        }
-        else {
+        } else {
             $this->populateDisabledPluginsFromDb();
             $this->writeDisabled();
         }
@@ -523,21 +554,22 @@ class PluginManager
     /**
      * Determines if a plugin is disabled by looking at the meta information
      * or the application configuration.
-     * @return boolean
+     *
+     * @param string|PluginBase $id
+     * @return bool
      */
     public function isDisabled($id)
     {
         $code = $this->getIdentifier($id);
+        $normalized = $this->normalizeIdentifier($code);
 
-        if (array_key_exists($code, $this->disabledPlugins)) {
-            return true;
-        }
-
-        return false;
+        return isset($this->disabledPlugins[$normalized]);
     }
 
     /**
      * Write the disabled plugins to a meta file.
+     *
+     * @return void
      */
     protected function writeDisabled()
     {
@@ -546,6 +578,7 @@ class PluginManager
 
     /**
      * Populates information about disabled plugins from database
+     *
      * @return void
      */
     protected function populateDisabledPluginsFromDb()
@@ -567,13 +600,15 @@ class PluginManager
 
     /**
      * Disables a single plugin in the system.
-     * @param string $id Plugin code/namespace
-     * @param bool $isUser Set to true if disabled by the user
-     * @return bool
+     *
+     * @param string|PluginBase $id Plugin code/namespace
+     * @param bool $isUser Set to true if disabled by the user, false by default
+     * @return bool Returns false if the plugin was already disabled, true otherwise
      */
     public function disablePlugin($id, $isUser = false)
     {
         $code = $this->getIdentifier($id);
+        $code = $this->normalizeIdentifier($code);
         if (array_key_exists($code, $this->disabledPlugins)) {
             return false;
         }
@@ -590,13 +625,15 @@ class PluginManager
 
     /**
      * Enables a single plugin in the system.
-     * @param string $id Plugin code/namespace
-     * @param bool $isUser Set to true if enabled by the user
-     * @return bool
+     *
+     * @param string|PluginBase $id Plugin code/namespace
+     * @param bool $isUser Set to true if enabled by the user, false by default
+     * @return bool Returns false if the plugin wasn't already disabled or if the user disabled a plugin that the system is trying to re-enable, true otherwise
      */
     public function enablePlugin($id, $isUser = false)
     {
         $code = $this->getIdentifier($id);
+        $code = $this->normalizeIdentifier($code);
         if (!array_key_exists($code, $this->disabledPlugins)) {
             return false;
         }
@@ -654,6 +691,7 @@ class PluginManager
     /**
      * Cross checks all plugins and their dependancies, if not met plugins
      * are disabled and vice versa.
+     *
      * @return void
      */
     protected function loadDependencies()
@@ -668,16 +706,14 @@ class PluginManager
             foreach ($required as $require) {
                 if (!$pluginObj = $this->findByIdentifier($require)) {
                     $disable = true;
-                }
-                elseif ($pluginObj->disabled) {
+                } elseif ($pluginObj->disabled) {
                     $disable = true;
                 }
             }
 
             if ($disable) {
                 $this->disablePlugin($id);
-            }
-            else {
+            } else {
                 $this->enablePlugin($id);
             }
         }
@@ -686,7 +722,9 @@ class PluginManager
     /**
      * Sorts a collection of plugins, in the order that they should be actioned,
      * according to their given dependencies. Least dependent come first.
-     * @return array Collection of sorted plugin identifiers
+     *
+     * @return array Array of sorted plugin identifiers and instantiated classes ['Author.Plugin' => PluginBase]
+     * @throws SystemException If a possible circular dependency is detected
      */
     protected function sortDependencies()
     {
@@ -708,7 +746,7 @@ class PluginManager
                 /*
                  * Get dependencies and remove any aliens
                  */
-                $depends = $this->getDependencies($plugin) ?: [];
+                $depends = $this->getDependencies($plugin);
                 $depends = array_filter($depends, function ($pluginCode) {
                     return isset($this->plugins[$pluginCode]);
                 });
@@ -752,17 +790,18 @@ class PluginManager
 
     /**
      * Returns the plugin identifiers that are required by the supplied plugin.
+     *
      * @param  string $plugin Plugin identifier, object or class
      * @return array
      */
     public function getDependencies($plugin)
     {
         if (is_string($plugin) && (!$plugin = $this->findByIdentifier($plugin))) {
-            return false;
+            return [];
         }
 
         if (!isset($plugin->require) || !$plugin->require) {
-            return null;
+            return [];
         }
 
         return is_array($plugin->require) ? $plugin->require : [$plugin->require];
@@ -785,6 +824,7 @@ class PluginManager
 
     /**
      * Completely roll back and delete a plugin from the system.
+     *
      * @param string $id Plugin code/namespace
      * @return void
      */
@@ -805,6 +845,7 @@ class PluginManager
 
     /**
      * Tears down a plugin's database tables and rebuilds them.
+     *
      * @param string $id Plugin code/namespace
      * @return void
      */