Merge branch 'floxglove-3' into saravea

Conflicts:
	.gitmodules

69 files changed, 619 insertions, 378 deletions

diff --git a/engine/classes/ElggAnnotation.php b/engine/classes/ElggAnnotation.php
index 511b5151f..175e7049d 100644
--- a/engine/classes/ElggAnnotation.php
+++ b/engine/classes/ElggAnnotation.php
@@ -11,6 +11,9 @@
  * @package    Elgg.Core
  * @subpackage DataModel.Annotations
  * @link       http://docs.elgg.org/DataModel/Annotations
+ *
+ * @property string $value_type
+ * @property string $enabled
  */
 class ElggAnnotation extends ElggExtender {
 
@@ -56,6 +59,8 @@ class ElggAnnotation extends ElggExtender {
 	 * Save this instance
 	 *
 	 * @return int an object id
+	 *
+	 * @throws IOException
 	 */
 	function save() {
 		if ($this->id > 0) {
diff --git a/engine/classes/ElggAttributeLoader.php b/engine/classes/ElggAttributeLoader.php
index 602bb8bae..2d1c1abde 100644
--- a/engine/classes/ElggAttributeLoader.php
+++ b/engine/classes/ElggAttributeLoader.php
@@ -148,11 +148,11 @@ class ElggAttributeLoader {
 				if (!is_callable($this->primary_loader)) {
 					throw new LogicException('Primary attribute loader must be callable');
 				}
-				if (!$this->requires_access_control) {
+				if ($this->requires_access_control) {
+					$fetched = (array) call_user_func($this->primary_loader, $row['guid']);
+				} else {
 					$ignoring_access = elgg_set_ignore_access();
-				}
-				$fetched = (array) call_user_func($this->primary_loader, $row['guid']);
-				if (!$this->requires_access_control) {
+					$fetched = (array) call_user_func($this->primary_loader, $row['guid']);
 					elgg_set_ignore_access($ignoring_access);
 				}
 				if (!$fetched) {
diff --git a/engine/classes/ElggAutoP.php b/engine/classes/ElggAutoP.php
index 89d77e583..f3c7cc972 100644
--- a/engine/classes/ElggAutoP.php
+++ b/engine/classes/ElggAutoP.php
@@ -117,6 +117,8 @@ class ElggAutoP {
 		// serialize back to HTML
 		$html = $this->_doc->saveHTML();
 
+		// Note: we create <autop> elements, which will later be converted to paragraphs
+
 		// split AUTOPs into multiples at /\n\n+/
 		$html = preg_replace('/(' . $this->_unique . 'NL){2,}/', '</autop><autop>', $html);
 		$html = str_replace(array($this->_unique . 'BR', $this->_unique . 'NL', '<br>'), 
@@ -134,6 +136,7 @@ class ElggAutoP {
 
 		// strip AUTOPs that only have comments/whitespace
 		foreach ($this->_xpath->query('//autop') as $autop) {
+			/* @var DOMElement $autop */
 			$hasContent = false;
 			if (trim($autop->textContent) !== '') {
 				$hasContent = true;
@@ -146,17 +149,19 @@ class ElggAutoP {
 				}
 			}
 			if (!$hasContent) {
-				// strip w/ preg_replace later (faster than moving nodes out)
+				// mark to be later replaced w/ preg_replace (faster than moving nodes out)
 				$autop->setAttribute("r", "1");
 			}
 		}
 
-		// remove a single AUTOP inside certain elements
+		// If a DIV contains a single AUTOP, remove it
 		foreach ($this->_xpath->query('//div') as $el) {
+			/* @var DOMElement $el */
 			$autops = $this->_xpath->query('./autop', $el);
 			if ($autops->length === 1) {
-				// strip w/ preg_replace later (faster than moving nodes out)
-				$autops->item(0)->setAttribute("r", "1");
+				$firstAutop = $autops->item(0);
+				/* @var DOMElement $firstAutop */
+				$firstAutop->setAttribute("r", "1");
 			}
 		}
 
@@ -185,7 +190,7 @@ class ElggAutoP {
 	 * @param DOMElement $el
 	 */
 	protected function _addParagraphs(DOMElement $el) {
-		// no need to recurse, just queue up
+		// no need to call recursively, just queue up
 		$elsToProcess = array($el);
 		$inlinesToProcess = array();
 		while ($el = array_shift($elsToProcess)) {
@@ -216,12 +221,12 @@ class ElggAutoP {
 
 				$isElement = ($node->nodeType === XML_ELEMENT_NODE);
 				if ($isElement) {
-					$elName = $node->nodeName;
+					$isBlock = in_array($node->nodeName, $this->_blocks);
+				} else {
+					$isBlock = false;
 				}
-				$isBlock = ($isElement && in_array($elName, $this->_blocks));
 
 				if ($alterInline) {
-					$isInline = $isElement && ! $isBlock;
 					$isText = ($node->nodeType === XML_TEXT_NODE);
 					$isLastInline = (! $node->nextSibling
 								   || ($node->nextSibling->nodeType === XML_ELEMENT_NODE
diff --git a/engine/classes/ElggBatch.php b/engine/classes/ElggBatch.php
index c1a77a0d9..5d59425d0 100644
--- a/engine/classes/ElggBatch.php
+++ b/engine/classes/ElggBatch.php
@@ -296,7 +296,8 @@ class ElggBatch
 	 * Increment the offset from the original options array? Setting to
 	 * false is required for callbacks that delete rows.
 	 *
-	 * @param bool $increment
+	 * @param bool $increment Set to false when deleting data
+	 * @return void
 	 */
 	public function setIncrementOffset($increment = true) {
 		$this->incrementOffset = (bool) $increment;
diff --git a/engine/classes/ElggData.php b/engine/classes/ElggData.php
index 3470ee1cf..426248ca3 100644
--- a/engine/classes/ElggData.php
+++ b/engine/classes/ElggData.php
@@ -5,6 +5,9 @@
  *
  * @package    Elgg.Core
  * @subpackage DataModel
+ *
+ * @property int $owner_guid
+ * @property int $time_created
  */
 abstract class ElggData implements
 	Loggable,	// Can events related to this object class be logged
@@ -33,14 +36,12 @@ abstract class ElggData implements
 	 *                        Passing false returns false.  Core constructors always pass false.
 	 *                        Does nothing either way since attributes are initialized by the time
 	 *                        this is called.
-	 * @return false|void False is
+	 * @return void
 	 * @deprecated 1.8 Use initializeAttributes()
 	 */
 	protected function initialise_attributes($pre18_api = true) {
 		if ($pre18_api) {
 			elgg_deprecated_notice('initialise_attributes() is deprecated by initializeAttributes()', 1.8);
-		} else {
-			return false;
 		}
 	}
 
@@ -111,7 +112,7 @@ abstract class ElggData implements
 	 * @param string $name  The attribute to set
 	 * @param mixed  $value The value to set it to
 	 *
-	 * @return The success of your set funtion?
+	 * @return bool The success of your set function?
 	 */
 	abstract protected function set($name, $value);
 
@@ -195,7 +196,7 @@ abstract class ElggData implements
 	 *
 	 * @see Iterator::current()
 	 *
-	 * @return void
+	 * @return mixed
 	 */
 	public function current() {
 		return current($this->attributes);
@@ -206,7 +207,7 @@ abstract class ElggData implements
 	 *
 	 * @see Iterator::key()
 	 *
-	 * @return void
+	 * @return string
 	 */
 	public function key() {
 		return key($this->attributes);
@@ -228,7 +229,7 @@ abstract class ElggData implements
 	 *
 	 * @see Iterator::valid()
 	 *
-	 * @return void
+	 * @return bool
 	 */
 	public function valid() {
 		return $this->valid;
@@ -266,12 +267,13 @@ abstract class ElggData implements
 	 *
 	 * @param mixed $key Name
 	 *
-	 * @return void
+	 * @return mixed
 	 */
 	public function offsetGet($key) {
 		if (array_key_exists($key, $this->attributes)) {
 			return $this->attributes[$key];
 		}
+		return null;
 	}
 
 	/**
diff --git a/engine/classes/ElggDiskFilestore.php b/engine/classes/ElggDiskFilestore.php
index 7aace43ba..7374aad35 100644
--- a/engine/classes/ElggDiskFilestore.php
+++ b/engine/classes/ElggDiskFilestore.php
@@ -60,6 +60,7 @@ class ElggDiskFilestore extends ElggFilestore {
 
 		$path = substr($fullname, 0, $ls);
 		$name = substr($fullname, $ls);
+		// @todo $name is unused, remove it or do we need to fix something?
 
 		// Try and create the directory
 		try {
@@ -108,7 +109,7 @@ class ElggDiskFilestore extends ElggFilestore {
 	 *
 	 * @param resource $f      File pointer resource
 	 * @param int      $length The number of bytes to read
-	 * @param inf      $offset The number of bytes to start after
+	 * @param int      $offset The number of bytes to start after
 	 *
 	 * @return mixed Contents of file or false on fail.
 	 */
@@ -198,6 +199,7 @@ class ElggDiskFilestore extends ElggFilestore {
 	 * @param ElggFile $file File object
 	 *
 	 * @return string The full path of where the file is stored
+	 * @throws InvalidParameterException
 	 */
 	public function getFilenameOnFilestore(ElggFile $file) {
 		$owner_guid = $file->getOwnerGuid();
@@ -315,8 +317,6 @@ class ElggDiskFilestore extends ElggFilestore {
 		} else {
 			return str_split($string);
 		}
-
-		return false;
 	}
 
 	/**
@@ -324,7 +324,7 @@ class ElggDiskFilestore extends ElggFilestore {
 	 *
 	 * @param int $identifier The guide of the entity to store the data under.
 	 *
-	 * @return str The path where the entity's data will be stored.
+	 * @return string The path where the entity's data will be stored.
 	 * @deprecated 1.8 Use ElggDiskFilestore::makeFileMatrix()
 	 */
 	protected function make_file_matrix($identifier) {
@@ -338,7 +338,7 @@ class ElggDiskFilestore extends ElggFilestore {
 	 *
 	 * @param int $guid The guide of the entity to store the data under.
 	 *
-	 * @return str The path where the entity's data will be stored.
+	 * @return string The path where the entity's data will be stored.
 	 */
 	protected function makeFileMatrix($guid) {
 		$entity = get_entity($guid);
@@ -363,7 +363,7 @@ class ElggDiskFilestore extends ElggFilestore {
 	 *
 	 * @param int $guid The entity to contrust a matrix for
 	 *
-	 * @return str The
+	 * @return string The
 	 */
 	protected function user_file_matrix($guid) {
 		elgg_deprecated_notice('ElggDiskFilestore::user_file_matrix() is deprecated by ::makeFileMatrix()', 1.8);
diff --git a/engine/classes/ElggEntity.php b/engine/classes/ElggEntity.php
index 929abceb2..f44e73023 100644
--- a/engine/classes/ElggEntity.php
+++ b/engine/classes/ElggEntity.php
@@ -34,6 +34,7 @@
  * @property int    $access_id      Specifies the visibility level of this entity
  * @property int    $time_created   A UNIX timestamp of when the entity was created (read-only, set on first save)
  * @property int    $time_updated   A UNIX timestamp of when the entity was last updated (automatically updated on save)
+ * @property-read string $enabled
  */
 abstract class ElggEntity extends ElggData implements
 	Notable,    // Calendar interface
@@ -940,7 +941,7 @@ abstract class ElggEntity extends ElggData implements
 	 * @param ElggMetadata $metadata  The piece of metadata to specifically check
 	 * @param int          $user_guid The user GUID, optionally (default: logged in user)
 	 *
-	 * @return true|false
+	 * @return bool
 	 */
 	function canEditMetadata($metadata = null, $user_guid = 0) {
 		return can_edit_entity_metadata($this->getGUID(), $user_guid, $metadata);
@@ -1668,9 +1669,11 @@ abstract class ElggEntity extends ElggData implements
 	/**
 	 * Import data from an parsed ODD xml data array.
 	 *
-	 * @param array $data XML data
+	 * @param ODD $data XML data
 	 *
 	 * @return true
+	 *
+	 * @throws InvalidParameterException
 	 */
 	public function import(ODD $data) {
 		if (!($data instanceof ODDEntity)) {
@@ -1732,8 +1735,6 @@ abstract class ElggEntity extends ElggData implements
 	 * @return array
 	 */
 	public function getTags($tag_names = NULL) {
-		global $CONFIG;
-
 		if ($tag_names && !is_array($tag_names)) {
 			$tag_names = array($tag_names);
 		}
diff --git a/engine/classes/ElggExtender.php b/engine/classes/ElggExtender.php
index d94bad837..25aba354f 100644
--- a/engine/classes/ElggExtender.php
+++ b/engine/classes/ElggExtender.php
@@ -171,7 +171,7 @@ abstract class ElggExtender extends ElggData {
 	public function export() {
 		$uuid = get_uuid_from_object($this);
 
-		$meta = new ODDMetadata($uuid, guid_to_uuid($this->entity_guid), $this->attributes['name'],
+		$meta = new ODDMetaData($uuid, guid_to_uuid($this->entity_guid), $this->attributes['name'],
 			$this->attributes['value'], $this->attributes['type'], guid_to_uuid($this->owner_guid));
 		$meta->setAttribute('published', date("r", $this->time_created));
 
diff --git a/engine/classes/ElggFile.php b/engine/classes/ElggFile.php
index f21621ffd..3e9c24c17 100644
--- a/engine/classes/ElggFile.php
+++ b/engine/classes/ElggFile.php
@@ -93,6 +93,7 @@ class ElggFile extends ElggObject {
 			$container_guid = $this->container_guid;
 		}
 		$fs = $this->getFilestore();
+		// @todo add getSize() to ElggFilestore
 		return $fs->getSize($prefix, $container_guid);
 	}
 
@@ -127,9 +128,11 @@ class ElggFile extends ElggObject {
 	 * @param mixed $default A default. Useful to pass what the browser thinks it is.
 	 * @since 1.7.12
 	 *
+	 * @note If $file is provided, this may be called statically
+	 *
 	 * @return mixed Detected type on success, false on failure.
 	 */
-	static function detectMimeType($file = null, $default = null) {
+	public function detectMimeType($file = null, $default = null) {
 		if (!$file) {
 			if (isset($this) && $this->filename) {
 				$file = $this->filename;
@@ -178,6 +181,8 @@ class ElggFile extends ElggObject {
 	 * @param string $mode Either read/write/append
 	 *
 	 * @return resource File handler
+	 *
+	 * @throws IOException|InvalidParameterException
 	 */
 	public function open($mode) {
 		if (!$this->getFilename()) {
@@ -285,6 +290,7 @@ class ElggFile extends ElggObject {
 	public function seek($position) {
 		$fs = $this->getFilestore();
 
+		// @todo add seek() to ElggFilestore
 		return $fs->seek($this->handle, $position);
 	}
 
@@ -347,6 +353,8 @@ class ElggFile extends ElggObject {
 	 * a filestore as recorded in metadata or the system default.
 	 *
 	 * @return ElggFilestore
+	 *
+	 * @throws ClassNotFoundException
 	 */
 	protected function getFilestore() {
 		// Short circuit if already set.
@@ -359,7 +367,6 @@ class ElggFile extends ElggObject {
 		// need to get all filestore::* metadata because the rest are "parameters" that
 		// get passed to filestore::setParameters()
 		if ($this->guid) {
-			$db_prefix = elgg_get_config('dbprefix');
 			$options = array(
 				'guid' => $this->guid,
 				'where' => array("n.string LIKE 'filestore::%'"),
@@ -388,6 +395,7 @@ class ElggFile extends ElggObject {
 
 			$this->filestore = new $filestore();
 			$this->filestore->setParameters($parameters);
+			// @todo explain why $parameters will always be set here (PhpStorm complains)
 		}
 
 		// this means the entity hasn't been saved so fallback to default
diff --git a/engine/classes/ElggFileCache.php b/engine/classes/ElggFileCache.php
index 34178d452..e654f1db2 100644
--- a/engine/classes/ElggFileCache.php
+++ b/engine/classes/ElggFileCache.php
@@ -13,6 +13,8 @@ class ElggFileCache extends ElggCache {
 	 * @param string $cache_path The cache path.
 	 * @param int    $max_age    Maximum age in seconds, 0 if no limit.
 	 * @param int    $max_size   Maximum size of cache in seconds, 0 if no limit.
+	 *
+	 * @throws ConfigurationException
 	 */
 	function __construct($cache_path, $max_age = 0, $max_size = 0) {
 		$this->setVariable("cache_path", $cache_path);
diff --git a/engine/classes/ElggGroup.php b/engine/classes/ElggGroup.php
index ea257f368..61f699f1a 100644
--- a/engine/classes/ElggGroup.php
+++ b/engine/classes/ElggGroup.php
@@ -32,7 +32,7 @@ class ElggGroup extends ElggEntity
 	 * @param mixed $guid If an int, load that GUID.
 	 * 	If an entity table db row, then will load the rest of the data.
 	 *
-	 * @throws Exception if there was a problem creating the group.
+	 * @throws IOException|InvalidParameterException if there was a problem creating the group.
 	 */
 	function __construct($guid = null) {
 		$this->initializeAttributes();
@@ -220,6 +220,7 @@ class ElggGroup extends ElggEntity
 	 * @return array|false
 	 */
 	public function getObjects($subtype = "", $limit = 10, $offset = 0) {
+		// @todo are we deprecating this method, too?
 		return get_objects_in_group($this->getGUID(), $subtype, 0, 0, "", $limit, $offset, false);
 	}
 
@@ -233,6 +234,7 @@ class ElggGroup extends ElggEntity
 	 * @return array|false
 	 */
 	public function getFriendsObjects($subtype = "", $limit = 10, $offset = 0) {
+		// @todo are we deprecating this method, too?
 		return get_objects_in_group($this->getGUID(), $subtype, 0, 0, "", $limit, $offset, false);
 	}
 
@@ -244,6 +246,7 @@ class ElggGroup extends ElggEntity
 	 * @return array|false
 	 */
 	public function countObjects($subtype = "") {
+		// @todo are we deprecating this method, too?
 		return get_objects_in_group($this->getGUID(), $subtype, 0, 0, "", 10, 0, true);
 	}
 
@@ -284,7 +287,7 @@ class ElggGroup extends ElggEntity
 	 *
 	 * @return bool
 	 */
-	public function isMember($user = 0) {
+	public function isMember($user = null) {
 		if (!($user instanceof ElggUser)) {
 			$user = elgg_get_logged_in_user_entity();
 		}
diff --git a/engine/classes/ElggMemcache.php b/engine/classes/ElggMemcache.php
index d9539b9cb..91d50ab89 100644
--- a/engine/classes/ElggMemcache.php
+++ b/engine/classes/ElggMemcache.php
@@ -32,6 +32,8 @@ class ElggMemcache extends ElggSharedMemoryCache {
 	 *
 	 * @param string $namespace The namespace for this cache to write to -
 	 * note, namespaces of the same name are shared!
+	 *
+	 * @throws ConfigurationException
 	 */
 	function __construct($namespace = 'default') {
 		global $CONFIG;
diff --git a/engine/classes/ElggMenuBuilder.php b/engine/classes/ElggMenuBuilder.php
index d9a704dd9..f6ec9dcd3 100644
--- a/engine/classes/ElggMenuBuilder.php
+++ b/engine/classes/ElggMenuBuilder.php
@@ -8,6 +8,9 @@
  */
 class ElggMenuBuilder {
 
+	/**
+	 * @var ElggMenuItem[]
+	 */
 	protected $menu = array();
 
 	protected $selected = null;
@@ -15,7 +18,7 @@ class ElggMenuBuilder {
 	/**
 	 * ElggMenuBuilder constructor
 	 *
-	 * @param array $menu Array of ElggMenuItem objects
+	 * @param ElggMenuItem[] $menu Array of ElggMenuItem objects
 	 */
 	public function __construct(array $menu) {
 		$this->menu = $menu;
@@ -107,6 +110,7 @@ class ElggMenuBuilder {
 			$children = array();
 			// divide base nodes from children
 			foreach ($section as $menu_item) {
+				/* @var ElggMenuItem $menu_item */
 				$parent_name = $menu_item->getParentName();
 				if (!$parent_name) {
 					$parents[$menu_item->getName()] = $menu_item;
@@ -118,6 +122,7 @@ class ElggMenuBuilder {
 			// attach children to parents
 			$iteration = 0;
 			$current_gen = $parents;
+			$next_gen = null;
 			while (count($children) && $iteration < 5) {
 				foreach ($children as $index => $menu_item) {
 					$parent_name = $menu_item->getParentName();
@@ -216,12 +221,12 @@ class ElggMenuBuilder {
 				array_push($stack, $root);
 				while (!empty($stack)) {
 					$node = array_pop($stack);
+					/* @var ElggMenuItem $node */
 					$node->sortChildren($sort_callback);
 					$children = $node->getChildren();
 					if ($children) {
 						$stack = array_merge($stack, $children);
 					}
-					$p = count($stack);
 				}
 			}
 		}
@@ -269,6 +274,8 @@ class ElggMenuBuilder {
 	 * @param ElggMenuItem $a
 	 * @param ElggMenuItem $b
 	 * @return bool
+	 *
+	 * @todo change name to compareByPriority
 	 */
 	public static function compareByWeight($a, $b) {
 		$aw = $a->getWeight();
diff --git a/engine/classes/ElggMetadata.php b/engine/classes/ElggMetadata.php
index 7f45dc3ea..3a8e2d817 100644
--- a/engine/classes/ElggMetadata.php
+++ b/engine/classes/ElggMetadata.php
@@ -6,6 +6,10 @@
  *
  * @package    Elgg.Core
  * @subpackage Metadata
+ *
+ * @property string $value_type
+ * @property int $owner_guid
+ * @property string $enabled
  */
 class ElggMetadata extends ElggExtender {
 
diff --git a/engine/classes/ElggPlugin.php b/engine/classes/ElggPlugin.php
index 8f71b79a8..ae447bddb 100644
--- a/engine/classes/ElggPlugin.php
+++ b/engine/classes/ElggPlugin.php
@@ -145,7 +145,7 @@ class ElggPlugin extends ElggObject {
 	/**
 	 * Sets the location of this plugin.
 	 *
-	 * @param path $id The path to the plugin's dir.
+	 * @param string $id The path to the plugin's dir.
 	 * @return bool
 	 */
 	public function setID($id) {
@@ -597,6 +597,8 @@ class ElggPlugin extends ElggObject {
 	 * Checks if this plugin can be activated on the current
 	 * Elgg installation.
 	 *
+	 * @todo remove $site_guid param or implement it
+	 *
 	 * @param mixed $site_guid Optional site guid
 	 * @return bool
 	 */
diff --git a/engine/classes/ElggPluginPackage.php b/engine/classes/ElggPluginPackage.php
index 2dc4bdb3d..209242288 100644
--- a/engine/classes/ElggPluginPackage.php
+++ b/engine/classes/ElggPluginPackage.php
@@ -100,7 +100,6 @@ class ElggPluginPackage {
 	 * @param string $plugin   The ID (directory name) or full path of the plugin.
 	 * @param bool   $validate Automatically run isValid()?
 	 *
-	 * @return true
 	 * @throws PluginException
 	 */
 	public function __construct($plugin, $validate = true) {
@@ -213,6 +212,7 @@ class ElggPluginPackage {
 			return false;
 		}
 
+		// Note: $conflicts and $requires are not unused. They're called dynamically
 		$conflicts = $this->getManifest()->getConflicts();
 		$requires = $this->getManifest()->getRequires();
 		$provides = $this->getManifest()->getProvides();
@@ -330,8 +330,10 @@ class ElggPluginPackage {
 	 * @return bool|array
 	 */
 	public function checkDependencies($full_report = false) {
+		// Note: $conflicts and $requires are not unused. They're called dynamically
 		$requires = $this->getManifest()->getRequires();
 		$conflicts = $this->getManifest()->getConflicts();
+
 		$enabled_plugins = elgg_get_plugins('active');
 		$this_id = $this->getID();
 		$report = array();
@@ -368,6 +370,7 @@ class ElggPluginPackage {
 		$check_types = array('requires', 'conflicts');
 
 		if ($full_report) {
+			// Note: $suggests is not unused. It's called dynamically
 			$suggests = $this->getManifest()->getSuggests();
 			$check_types[] = 'suggests';
 		}
diff --git a/engine/classes/ElggPriorityList.php b/engine/classes/ElggPriorityList.php
index 8a3b836a8..b5f8fe163 100644
--- a/engine/classes/ElggPriorityList.php
+++ b/engine/classes/ElggPriorityList.php
@@ -89,7 +89,7 @@
  *	return true;
  * }
  *
- * @package Elgg.Core
+ * @package    Elgg.Core
  * @subpackage Helpers
  */
 class ElggPriorityList
@@ -126,7 +126,9 @@ class ElggPriorityList
 	 *                        maintains its priority and the new element is to the next available
 	 *                        slot, taking into consideration all previously registered elements.
 	 *                        Negative elements are accepted.
+	 * @param bool  $exact    unused
 	 * @return int            The priority of the added element.
+	 * @todo remove $exact or implement it. Note we use variable name strict below.
 	 */
 	public function add($element, $priority = null, $exact = false) {
 		if ($priority !== null && !is_numeric($priority)) {
@@ -146,7 +148,8 @@ class ElggPriorityList
 	 * @warning The element must have the same attributes / values. If using $strict, it must have
 	 *          the same types. array(10) will fail in strict against array('10') (str vs int).
 	 *
-	 * @param type $element
+	 * @param mixed $element The element to remove from the list
+	 * @param bool  $strict  Whether to check the type of the element match
 	 * @return bool
 	 */
 	public function remove($element, $strict = false) {
@@ -162,10 +165,10 @@ class ElggPriorityList
 	/**
 	 * Move an existing element to a new priority.
 	 *
-	 * @param mixed  $current_priority
-	 * @param int    $new_priority
-	 *
-	 * @return int The new priority.
+	 * @param mixed  $element      The element to move
+	 * @param int    $new_priority The new priority for the element
+	 * @param bool   $strict       Whether to check the type of the element match
+	 * @return bool
 	 */
 	public function move($element, $new_priority, $strict = false) {
 		$new_priority = (int) $new_priority;
@@ -200,12 +203,12 @@ class ElggPriorityList
 	 *
 	 * If no user function is provided the elements are sorted by priority registered.
 	 *
-	 * The callback function should accept the array of elements as the first argument and should
-	 * return a sorted array.
+	 * The callback function should accept the array of elements as the first 
+	 * argument and should return a sorted array.
 	 *
 	 * This function can be called multiple times.
 	 *
-	 * @param type $callback
+	 * @param callback $callback The callback for sorting. Numeric sorting is the default.
 	 * @return bool
 	 */
 	public function sort($callback = null) {
@@ -268,7 +271,7 @@ class ElggPriorityList
 	/**
 	 * Returns the element at $priority.
 	 *
-	 * @param int $priority
+	 * @param int $priority The priority
 	 * @return mixed The element or false on fail.
 	 */
 	public function getElement($priority) {
diff --git a/engine/classes/ElggRelationship.php b/engine/classes/ElggRelationship.php
index efc0f7eff..d2e88882a 100644
--- a/engine/classes/ElggRelationship.php
+++ b/engine/classes/ElggRelationship.php
@@ -71,6 +71,7 @@ class ElggRelationship extends ElggData implements
 	 * Save the relationship
 	 *
 	 * @return int the relationship id
+	 * @throws IOException
 	 */
 	public function save() {
 		if ($this->id > 0) {
@@ -145,7 +146,7 @@ class ElggRelationship extends ElggData implements
 	 * @param ODD $data ODD data
 
 	 * @return bool
-	 * @throws ImportException
+	 * @throws ImportException|InvalidParameterException
 	 */
 	public function import(ODD $data) {
 		if (!($data instanceof ODDRelationship)) {
@@ -179,6 +180,8 @@ class ElggRelationship extends ElggData implements
 				return true;
 			}
 		}
+
+		return false;
 	}
 
 	// SYSTEM LOG INTERFACE ////////////////////////////////////////////////////////////
diff --git a/engine/classes/ElggSite.php b/engine/classes/ElggSite.php
index 1fe49b85c..1a34df195 100644
--- a/engine/classes/ElggSite.php
+++ b/engine/classes/ElggSite.php
@@ -381,7 +381,9 @@ class ElggSite extends ElggEntity {
 				elgg_register_plugin_hook_handler('index', 'system', 'elgg_walled_garden_index', 1);
 
 				if (!$this->isPublicPage()) {
-					$_SESSION['last_forward_from'] = current_page_url();
+					if (!elgg_is_xhr()) {
+						$_SESSION['last_forward_from'] = current_page_url();
+					}
 					register_error(elgg_echo('loggedinrequired'));
 					forward();
 				}
@@ -443,8 +445,6 @@ class ElggSite extends ElggEntity {
 		// include a hook for plugin authors to include public pages
 		$plugins = elgg_trigger_plugin_hook('public_pages', 'walled_garden', NULL, array());
 
-		// lookup admin-specific public pages
-
 		// allow public pages
 		foreach (array_merge($defaults, $plugins) as $public) {
 			$pattern = "`^{$CONFIG->url}$public/*$`i";
diff --git a/engine/classes/ElggWidget.php b/engine/classes/ElggWidget.php
index 99708f66a..c123e5032 100644
--- a/engine/classes/ElggWidget.php
+++ b/engine/classes/ElggWidget.php
@@ -7,6 +7,11 @@
  *
  * @package    Elgg.Core
  * @subpackage Widgets
+ *
+ * @property-read string $handler internal, do not use
+ * @property-read string $column internal, do not use
+ * @property-read string $order internal, do not use
+ * @property-read string $context internal, do not use
  */
 class ElggWidget extends ElggObject {
 
diff --git a/engine/classes/ElggXMLElement.php b/engine/classes/ElggXMLElement.php
index 65a13912c..4e4b7e63c 100644
--- a/engine/classes/ElggXMLElement.php
+++ b/engine/classes/ElggXMLElement.php
@@ -32,7 +32,7 @@ class ElggXMLElement {
 	}
 
 	/**
-	 * @return array:string The attributes
+	 * @return string[] The attributes
 	 */
 	public function getAttributes() {
 		//include namespace declarations as attributes
@@ -64,7 +64,7 @@ class ElggXMLElement {
 	}
 
 	/**
-	 * @return array:ElggXMLElement Child elements
+	 * @return ElggXMLElement[] Child elements
 	 */
 	public function getChildren() {
 		$children = $this->_element->children();
diff --git a/engine/classes/ODDMetaData.php b/engine/classes/ODDMetaData.php
index 58862e0fb..09b653582 100644
--- a/engine/classes/ODDMetaData.php
+++ b/engine/classes/ODDMetaData.php
@@ -10,12 +10,12 @@ class ODDMetaData extends ODD {
 	/**
 	 * New ODD metadata
 	 *
-	 * @param unknown_type $uuid        Unique ID
-	 * @param unknown_type $entity_uuid Another unique ID
-	 * @param unknown_type $name        Name
-	 * @param unknown_type $value       Value
-	 * @param unknown_type $type        Type
-	 * @param unknown_type $owner_uuid  Owner ID
+	 * @param string $uuid        Unique ID
+	 * @param string $entity_uuid Another unique ID
+	 * @param string $name        Name
+	 * @param string $value       Value
+	 * @param string $type        Type
+	 * @param string $owner_uuid  Owner ID
 	 */
 	function __construct($uuid, $entity_uuid, $name, $value, $type = "", $owner_uuid = "") {
 		parent::__construct();
@@ -31,7 +31,7 @@ class ODDMetaData extends ODD {
 	/**
 	 * Returns 'metadata'
 	 *
-	 * @return 'metadata'
+	 * @return string 'metadata'
 	 */
 	protected function getTagName() {
 		return "metadata";
diff --git a/engine/classes/ODDRelationship.php b/engine/classes/ODDRelationship.php
index 2906b1c73..8b1fe217b 100644
--- a/engine/classes/ODDRelationship.php
+++ b/engine/classes/ODDRelationship.php
@@ -10,9 +10,9 @@ class ODDRelationship extends ODD {
 	/**
 	 * New ODD Relationship
 	 *
-	 * @param unknown_type $uuid1 First UUID
-	 * @param unknown_type $type  Type of telationship
-	 * @param unknown_type $uuid2 Second UUId
+	 * @param string $uuid1 First UUID
+	 * @param string $type  Type of telationship
+	 * @param string $uuid2 Second UUId
 	 */
 	function __construct($uuid1, $type, $uuid2) {
 		parent::__construct();
@@ -25,7 +25,7 @@ class ODDRelationship extends ODD {
 	/**
 	 * Returns 'relationship'
 	 *
-	 * @return 'relationship'
+	 * @return string 'relationship'
 	 */
 	protected function getTagName() {
 		return "relationship";
diff --git a/engine/handlers/cache_handler.php b/engine/handlers/cache_handler.php
index 7706c2c92..9848d3531 100644
--- a/engine/handlers/cache_handler.php
+++ b/engine/handlers/cache_handler.php
@@ -93,7 +93,12 @@ if (file_exists($filename)) {
 	// someone trying to access a non-cached file or a race condition with cache flushing
 	mysql_close($mysql_dblink);
 	require_once(dirname(dirname(__FILE__)) . "/start.php");
-	elgg_regenerate_simplecache();
+
+	global $CONFIG;
+	if (!isset($CONFIG->views->simplecache[$view])) {
+		header("HTTP/1.1 404 Not Found");
+		exit;
+	}
 
 	elgg_set_viewtype($viewtype);
 	$contents = elgg_view($view);
diff --git a/engine/lib/access.php b/engine/lib/access.php
index f7d3bf7ea..de0693ea8 100644
--- a/engine/lib/access.php
+++ b/engine/lib/access.php
@@ -1015,6 +1015,10 @@ function access_init() {
  *
  * Returns true to override the access system or null if no change is needed.
  *
+ * @param string $hook
+ * @param string $type
+ * @param bool $value
+ * @param array $params
  * @return true|null
  * @access private
  */
@@ -1047,6 +1051,13 @@ function elgg_override_permissions($hook, $type, $value, $params) {
 
 /**
  * Runs unit tests for the entities object.
+ *
+ * @param string $hook
+ * @param string $type
+ * @param array $value
+ * @param array $params
+ * @return array
+ *
  * @access private
  */
 function access_test($hook, $type, $value, $params) {
diff --git a/engine/lib/actions.php b/engine/lib/actions.php
index 53b185dea..f78ca63df 100644
--- a/engine/lib/actions.php
+++ b/engine/lib/actions.php
@@ -65,12 +65,11 @@ function action($action, $forwarder = "") {
 	// @todo REMOVE THESE ONCE #1509 IS IN PLACE.
 	// Allow users to disable plugins without a token in order to
 	// remove plugins that are incompatible.
-	// Login and logout are for convenience.
+	// Logout for convenience.
 	// file/download (see #2010)
 	$exceptions = array(
 		'admin/plugins/disable',
 		'logout',
-		'login',
 		'file/download',
 	);
 
@@ -252,10 +251,20 @@ function validate_action_token($visibleerrors = TRUE, $token = NULL, $ts = NULL)
 					register_error(elgg_echo('actiongatekeeper:pluginprevents'));
 				}
 			} else if ($visibleerrors) {
-				register_error(elgg_echo('actiongatekeeper:timeerror'));
+				// this is necessary because of #5133
+				if (elgg_is_xhr()) {
+					register_error(elgg_echo('js:security:token_refresh_failed', array(elgg_get_site_url())));
+				} else {
+					register_error(elgg_echo('actiongatekeeper:timeerror'));
+				}
 			}
 		} else if ($visibleerrors) {
-			register_error(elgg_echo('actiongatekeeper:tokeninvalid'));
+			// this is necessary because of #5133
+			if (elgg_is_xhr()) {
+				register_error(elgg_echo('js:security:token_refresh_failed', array(elgg_get_site_url())));
+			} else {
+				register_error(elgg_echo('actiongatekeeper:tokeninvalid'));
+			}
 		}
 	} else {
 		if (! empty($_SERVER['CONTENT_LENGTH']) && empty($_POST)) {
diff --git a/engine/lib/admin.php b/engine/lib/admin.php
index 35ab5599d..ec19a5476 100644
--- a/engine/lib/admin.php
+++ b/engine/lib/admin.php
@@ -346,7 +346,7 @@ function elgg_admin_add_plugin_settings_menu() {
 	$active_plugins = elgg_get_plugins('active');
 	if (!$active_plugins) {
 		// nothing added because no items
-		return FALSE;
+		return;
 	}
 
 	foreach ($active_plugins as $plugin) {
@@ -380,6 +380,7 @@ function elgg_admin_add_plugin_settings_menu() {
  */
 function elgg_admin_sort_page_menu($hook, $type, $return, $params) {
 	$configure_items = $return['configure'];
+	/* @var ElggMenuItem[] $configure_items */
 	foreach ($configure_items as $menu_item) {
 		if ($menu_item->getName() == 'settings') {
 			$settings = $menu_item;
@@ -387,6 +388,7 @@ function elgg_admin_sort_page_menu($hook, $type, $return, $params) {
 	}
 
 	// keep the basic and advanced settings at the top
+	/* @var ElggMenuItem $settings */
 	$children = $settings->getChildren();
 	$site_settings = array_splice($children, 0, 2);
 	usort($children, array('ElggMenuBuilder', 'compareByText'));
@@ -552,7 +554,7 @@ function admin_plugin_screenshot_page_handler($pages) {
  *	* COPYRIGHT.txt
  *	* LICENSE.txt
  *
- * @param type $page
+ * @param array $pages
  * @return bool
  * @access private
  */
@@ -615,7 +617,11 @@ function admin_markdown_page_handler($pages) {
 /**
  * Adds default admin widgets to the admin dashboard.
  *
- * @return void
+ * @param string $event
+ * @param string $type
+ * @param ElggUser $user
+ *
+ * @return null|true
  * @access private
  */
 function elgg_add_admin_widgets($event, $type, $user) {
@@ -637,6 +643,7 @@ function elgg_add_admin_widgets($event, $type, $user) {
 			$guid = elgg_create_widget($user->getGUID(), $handler, 'admin');
 			if ($guid) {
 				$widget = get_entity($guid);
+				/* @var ElggWidget $widget */
 				$widget->move($column, $position);
 			}
 		}
diff --git a/engine/lib/annotations.php b/engine/lib/annotations.php
index 3b9f84703..bd5ea1a1f 100644
--- a/engine/lib/annotations.php
+++ b/engine/lib/annotations.php
@@ -17,6 +17,7 @@
  */
 function row_to_elggannotation($row) {
 	if (!($row instanceof stdClass)) {
+		// @todo should throw in this case?
 		return $row;
 	}
 
@@ -30,7 +31,7 @@ function row_to_elggannotation($row) {
  *
  * @param int $id The id of the annotation object being retrieved.
  *
- * @return false|ElggAnnotation
+ * @return ElggAnnotation|false
  */
 function elgg_get_annotation_from_id($id) {
 	return elgg_get_metastring_based_object_from_id($id, 'annotations');
@@ -195,10 +196,22 @@ function update_annotation($annotation_id, $name, $value, $value_type, $owner_gu
  *                                   for the proper use of the "calculation" option.
  *
  *
- * @return mixed
+ * @return ElggAnnotation[]|mixed
  * @since 1.8.0
  */
 function elgg_get_annotations(array $options = array()) {
+
+	// @todo remove support for count shortcut - see #4393
+	if (isset($options['__egefac']) && $options['__egefac']) {
+		unset($options['__egefac']);
+	} else {
+		// support shortcut of 'count' => true for 'annotation_calculation' => 'count'
+		if (isset($options['count']) && $options['count']) {
+			$options['annotation_calculation'] = 'count';
+			unset($options['count']);
+		}		
+	}
+	
 	$options['metastring_type'] = 'annotations';
 	return elgg_get_metastring_based_objects($options);
 }
@@ -424,6 +437,10 @@ function elgg_get_entities_from_annotation_calculation($options) {
 
 	$options['callback'] = 'entity_row_to_elggstar';
 
+	// see #4393
+	// @todo remove after the 'count' shortcut is removed from elgg_get_annotations()
+	$options['__egefac'] = true;
+
 	return elgg_get_annotations($options);
 }
 
@@ -441,19 +458,20 @@ function elgg_list_entities_from_annotation_calculation($options) {
 }
 
 /**
- * Handler called by trigger_plugin_hook on the "export" event.
+ * Export the annotations for the specified entity
  *
  * @param string $hook        'export'
- * @param string $entity_type 'all'
+ * @param string $type        'all'
  * @param mixed  $returnvalue Default return value
- * @param mixed  $params      List of params to export
+ * @param mixed  $params      Parameters determining what annotations to export
  *
  * @elgg_plugin_hook export all
  *
- * @return mixed
+ * @return array
+ * @throws InvalidParameterException
  * @access private
  */
-function export_annotation_plugin_hook($hook, $entity_type, $returnvalue, $params) {
+function export_annotation_plugin_hook($hook, $type, $returnvalue, $params) {
 	// Sanity check values
 	if ((!is_array($params)) && (!isset($params['guid']))) {
 		throw new InvalidParameterException(elgg_echo('InvalidParameterException:GUIDNotForExport'));
@@ -464,12 +482,12 @@ function export_annotation_plugin_hook($hook, $entity_type, $returnvalue, $param
 	}
 
 	$guid = (int)$params['guid'];
-	$name = $params['name'];
+	$options = array('guid' => $guid, 'limit' => 0);
+	if (isset($params['name'])) {
+		$options['annotation_name'] = $params['name'];
+	}
 
-	$result = elgg_get_annotations(array(
-		'guid' => $guid,
-		'limit' => 0
-	));
+	$result = elgg_get_annotations($options);
 
 	if ($result) {
 		foreach ($result as $r) {
@@ -541,6 +559,7 @@ function elgg_comment_url_handler(ElggAnnotation $comment) {
 	if ($entity) {
 		return $entity->getURL() . '#item-annotation-' . $comment->id;
 	}
+	return "";
 }
 
 /**
@@ -557,6 +576,12 @@ function elgg_register_annotation_url_handler($extender_name = "all", $function_
 
 /**
  * Register annotation unit tests
+ *
+ * @param string $hook
+ * @param string $type
+ * @param array $value
+ * @param array $params
+ * @return array
  * @access private
  */
 function annotations_test($hook, $type, $value, $params) {
diff --git a/engine/lib/cache.php b/engine/lib/cache.php
index be1c43e14..59359124e 100644
--- a/engine/lib/cache.php
+++ b/engine/lib/cache.php
@@ -125,7 +125,7 @@ function elgg_get_filepath_cache() {
  * @access private
  */
 function elgg_filepath_cache_reset() {
-	return elgg_reset_system_cache();
+	elgg_reset_system_cache();
 }
 /**
  * @access private
@@ -143,13 +143,13 @@ function elgg_filepath_cache_load($type) {
  * @access private
  */
 function elgg_enable_filepath_cache() {
-	return elgg_enable_system_cache();
+	elgg_enable_system_cache();
 }
 /**
  * @access private
  */
 function elgg_disable_filepath_cache() {
-	return elgg_disable_system_cache();
+	elgg_disable_system_cache();
 }
 
 /* Simplecache */
@@ -222,7 +222,7 @@ function elgg_get_simplecache_url($type, $view) {
 /**
  * Regenerates the simple cache.
  *
- * @warning This does not invalidate the cache, but actively resets it.
+ * @warning This does not invalidate the cache, but actively rebuilds it.
  *
  * @param string $viewtype Optional viewtype to regenerate. Defaults to all valid viewtypes.
  *
@@ -444,7 +444,7 @@ function _elgg_cache_init() {
 	if ($CONFIG->system_cache_enabled && !$CONFIG->i18n_loaded_from_cache) {
 		reload_all_translations();
 		foreach ($CONFIG->translations as $lang => $map) {
-			elgg_save_system_cache("$lang.php", serialize($map));
+			elgg_save_system_cache("$lang.lang", serialize($map));
 		}
 	}
 }
diff --git a/engine/lib/calendar.php b/engine/lib/calendar.php
index 9a06c5292..e6f95934c 100644
--- a/engine/lib/calendar.php
+++ b/engine/lib/calendar.php
@@ -39,6 +39,8 @@ function get_day_end($day = null, $month = null, $year = null) {
 /**
  * Return the notable entities for a given time period.
  *
+ * @todo this function also accepts an array(type => subtypes) for 3rd arg. Should we document this?
+ *
  * @param int     $start_time     The start time as a unix timestamp.
  * @param int     $end_time       The end time as a unix timestamp.
  * @param string  $type           The type of entity (eg "user", "object" etc)
diff --git a/engine/lib/configuration.php b/engine/lib/configuration.php
index b10e51130..a0f297f0c 100644
--- a/engine/lib/configuration.php
+++ b/engine/lib/configuration.php
@@ -36,6 +36,7 @@ function elgg_get_site_url($site_guid = 0) {
 	if (!$site instanceof ElggSite) {
 		return false;
 	}
+	/* @var ElggSite $site */
 
 	return $site->url;
 }
@@ -138,7 +139,7 @@ function elgg_set_config($name, $value) {
 /**
  * Save a configuration setting
  *
- * @param string $name      Configuration name (cannot be greater than 32 characters)
+ * @param string $name      Configuration name (cannot be greater than 255 characters)
  * @param mixed  $value     Configuration value. Should be string for installation setting
  * @param int    $site_guid NULL for installation setting, 0 for default site
  *
@@ -173,7 +174,7 @@ function elgg_save_config($name, $value, $site_guid = 0) {
 /**
  * Check that installation has completed and the database is populated.
  *
- * @throws InstallationException
+ * @throws InstallationException|DatabaseException
  * @return void
  * @access private
  */
@@ -181,7 +182,7 @@ function verify_installation() {
 	global $CONFIG;
 
 	if (isset($CONFIG->installed)) {
-		return $CONFIG->installed;
+		return;
 	}
 
 	try {
@@ -227,9 +228,9 @@ function datalist_get($name) {
 
 	$name = trim($name);
 
-	// cannot store anything longer than 32 characters in db, so catch here
-	if (elgg_strlen($name) > 32) {
-		elgg_log("The name length for configuration variables cannot be greater than 32", "ERROR");
+	// cannot store anything longer than 255 characters in db, so catch here
+	if (elgg_strlen($name) > 255) {
+		elgg_log("The name length for configuration variables cannot be greater than 255", "ERROR");
 		return false;
 	}
 
@@ -286,7 +287,7 @@ function datalist_get($name) {
 function datalist_set($name, $value) {
 	global $CONFIG, $DATALIST_CACHE;
 
-	// cannot store anything longer than 32 characters in db, so catch before we set
+	// cannot store anything longer than 255 characters in db, so catch before we set
 	if (elgg_strlen($name) > 255) {
 		elgg_log("The name length for configuration variables cannot be greater than 255", "ERROR");
 		return false;
@@ -332,7 +333,7 @@ function datalist_set($name, $value) {
  * This will cause the run once function to be run on all installations.  To perform
  * additional upgrades, create new functions for each release.
  *
- * @warning The function name cannot be longer than 32 characters long due to
+ * @warning The function name cannot be longer than 255 characters long due to
  * the current schema for the datalist table.
  *
  * @internal A datalist entry $functioname is created with the value of time().
@@ -407,7 +408,7 @@ function unset_config($name, $site_guid = 0) {
  * @param string $value     Its value
  * @param int    $site_guid Optionally, the GUID of the site (current site is assumed by default)
  *
- * @return 0
+ * @return bool
  * @todo The config table doens't have numeric primary keys so insert_data returns 0.
  * @todo Use "INSERT ... ON DUPLICATE KEY UPDATE" instead of trying to delete then add.
  * @see unset_config()
@@ -419,9 +420,9 @@ function set_config($name, $value, $site_guid = 0) {
 
 	$name = trim($name);
 
-	// cannot store anything longer than 32 characters in db, so catch before we set
-	if (elgg_strlen($name) > 32) {
-		elgg_log("The name length for configuration variables cannot be greater than 32", "ERROR");
+	// cannot store anything longer than 255 characters in db, so catch before we set
+	if (elgg_strlen($name) > 255) {
+		elgg_log("The name length for configuration variables cannot be greater than 255", "ERROR");
 		return false;
 	}
 
diff --git a/engine/lib/cron.php b/engine/lib/cron.php
index f7a032f4a..4f3d05b93 100644
--- a/engine/lib/cron.php
+++ b/engine/lib/cron.php
@@ -26,11 +26,10 @@ function cron_init() {
  * @param array $page Pages
  *
  * @return bool
+ * @throws CronException
  * @access private
  */
 function cron_page_handler($page) {
-	global $CONFIG;
-
 	if (!isset($page[0])) {
 		forward();
 	}
@@ -51,7 +50,6 @@ function cron_page_handler($page) {
 	$params['time'] = time();
 
 	// Data to return to
-	$std_out = "";
 	$old_stdout = "";
 	ob_start();
 
diff --git a/engine/lib/database.php b/engine/lib/database.php
index 7d90b30b8..2b348366d 100644
--- a/engine/lib/database.php
+++ b/engine/lib/database.php
@@ -17,7 +17,9 @@
  * $DB_QUERY_CACHE[$query] => array(result1, result2, ... resultN)
  * </code>
  *
- * @global array $DB_QUERY_CACHE
+ * @warning be array this var may be an array or ElggStaticVariableCache depending on when called :(
+ *
+ * @global ElggStaticVariableCache|array $DB_QUERY_CACHE
  */
 global $DB_QUERY_CACHE;
 $DB_QUERY_CACHE = array();
@@ -48,7 +50,7 @@ $DB_DELAYED_QUERIES = array();
  * Each database link created with establish_db_link($name) is stored in
  * $dblink as $dblink[$name] => resource.  Use get_db_link($name) to retrieve it.
  *
- * @global array $dblink
+ * @global resource[] $dblink
  */
 global $dblink;
 $dblink = array();
@@ -72,11 +74,12 @@ $dbcalls = 0;
  * resource. eg "read", "write", or "readwrite".
  *
  * @return void
+ * @throws DatabaseException
  * @access private
  */
 function establish_db_link($dblinkname = "readwrite") {
 	// Get configuration, and globalise database link
-	global $CONFIG, $dblink, $DB_QUERY_CACHE, $dbcalls;
+	global $CONFIG, $dblink, $DB_QUERY_CACHE;
 
 	if ($dblinkname != "readwrite" && isset($CONFIG->db[$dblinkname])) {
 		if (is_array($CONFIG->db[$dblinkname])) {
@@ -120,6 +123,8 @@ function establish_db_link($dblinkname = "readwrite") {
 
 	// Set up cache if global not initialized and query cache not turned off
 	if ((!$DB_QUERY_CACHE) && (!$db_cache_off)) {
+		// @todo everywhere else this is assigned to array(), making it dangerous to call
+		// object methods on this. We should consider making this an plain array
 		$DB_QUERY_CACHE = new ElggStaticVariableCache('db_query_cache');
 	}
 }
@@ -134,7 +139,7 @@ function establish_db_link($dblinkname = "readwrite") {
  * @access private
  */
 function setup_db_connections() {
-	global $CONFIG, $dblink;
+	global $CONFIG;
 
 	if (!empty($CONFIG->db->split)) {
 		establish_db_link('read');
@@ -197,7 +202,7 @@ function db_delayedexecution_shutdown_hook() {
  *
  * @param string $dblinktype The type of link we want: "read", "write" or "readwrite".
  *
- * @return object Database link
+ * @return resource Database link
  * @access private
  */
 function get_db_link($dblinktype) {
@@ -216,7 +221,7 @@ function get_db_link($dblinktype) {
 /**
  * Execute an EXPLAIN for $query.
  *
- * @param str   $query The query to explain
+ * @param string $query The query to explain
  * @param mixed $link  The database link resource to user.
  *
  * @return mixed An object of the query's result, or FALSE
@@ -240,14 +245,14 @@ function explain_query($query, $link) {
  * {@link $dbcalls} is incremented and the query is saved into the {@link $DB_QUERY_CACHE}.
  *
  * @param string $query  The query
- * @param link   $dblink The DB link
+ * @param resource   $dblink The DB link
  *
- * @return The result of mysql_query()
+ * @return resource result of mysql_query()
  * @throws DatabaseException
  * @access private
  */
 function execute_query($query, $dblink) {
-	global $CONFIG, $dbcalls;
+	global $dbcalls;
 
 	if ($query == NULL) {
 		throw new DatabaseException(elgg_echo('DatabaseException:InvalidQuery'));
@@ -275,7 +280,7 @@ function execute_query($query, $dblink) {
  * the raw result from {@link mysql_query()}.
  *
  * @param string   $query   The query to execute
- * @param resource $dblink  The database link to use or the link type (read | write)
+ * @param resource|string $dblink  The database link to use or the link type (read | write)
  * @param string   $handler A callback function to pass the results array to
  *
  * @return true
@@ -386,7 +391,7 @@ function get_data_row($query, $callback = "") {
  * @access private
  */
 function elgg_query_runner($query, $callback = null, $single = false) {
-	global $CONFIG, $DB_QUERY_CACHE;
+	global $DB_QUERY_CACHE;
 
 	// Since we want to cache results of running the callback, we need to
 	// need to namespace the query with the callback and single result request.
@@ -410,7 +415,7 @@ function elgg_query_runner($query, $callback = null, $single = false) {
 
 		// test for callback once instead of on each iteration.
 		// @todo check profiling to see if this needs to be broken out into
-		// explicit cases instead of checking in the interation.
+		// explicit cases instead of checking in the iteration.
 		$is_callable = is_callable($callback);
 		while ($row = mysql_fetch_object($result)) {
 			if ($is_callable) {
@@ -451,7 +456,7 @@ function elgg_query_runner($query, $callback = null, $single = false) {
  * @access private
  */
 function insert_data($query) {
-	global $CONFIG, $DB_QUERY_CACHE;
+	global $DB_QUERY_CACHE;
 
 	elgg_log("DB query $query", 'NOTICE');
 	
@@ -459,6 +464,7 @@ function insert_data($query) {
 
 	// Invalidate query cache
 	if ($DB_QUERY_CACHE) {
+		/* @var ElggStaticVariableCache $DB_QUERY_CACHE */
 		$DB_QUERY_CACHE->clear();
 	}
 
@@ -482,7 +488,7 @@ function insert_data($query) {
  * @access private
  */
 function update_data($query) {
-	global $CONFIG, $DB_QUERY_CACHE;
+	global $DB_QUERY_CACHE;
 
 	elgg_log("DB query $query", 'NOTICE');
 
@@ -490,6 +496,7 @@ function update_data($query) {
 
 	// Invalidate query cache
 	if ($DB_QUERY_CACHE) {
+		/* @var ElggStaticVariableCache $DB_QUERY_CACHE */
 		$DB_QUERY_CACHE->clear();
 		elgg_log("Query cache invalidated", 'NOTICE');
 	}
@@ -512,7 +519,7 @@ function update_data($query) {
  * @access private
  */
 function delete_data($query) {
-	global $CONFIG, $DB_QUERY_CACHE;
+	global $DB_QUERY_CACHE;
 
 	elgg_log("DB query $query", 'NOTICE');
 
@@ -520,6 +527,7 @@ function delete_data($query) {
 
 	// Invalidate query cache
 	if ($DB_QUERY_CACHE) {
+		/* @var ElggStaticVariableCache $DB_QUERY_CACHE */
 		$DB_QUERY_CACHE->clear();
 		elgg_log("Query cache invalidated", 'NOTICE');
 	}
@@ -638,7 +646,7 @@ function run_sql_script($scriptlocation) {
 			$statement = str_replace("prefix_", $CONFIG->dbprefix, $statement);
 			if (!empty($statement)) {
 				try {
-					$result = update_data($statement);
+					update_data($statement);
 				} catch (DatabaseException $e) {
 					$errors[] = $e->getMessage();
 				}
diff --git a/engine/lib/deprecated-1.8.php b/engine/lib/deprecated-1.8.php
index 4b9d41543..2b4ffcc4f 100644
--- a/engine/lib/deprecated-1.8.php
+++ b/engine/lib/deprecated-1.8.php
@@ -87,7 +87,7 @@ function list_entities_from_access_id($access_id, $entity_type = "", $entity_sub
 	elgg_deprecated_notice("All list_entities* functions were deprecated in 1.8.  Use elgg_list_entities* instead.", 1.8);
 
 	echo elgg_list_entities_from_access_id(array('access_id' => $access_id,
-		'types' => $entity_type, 'subtypes' => $entity_subtype, 'owner_guids' => $owner_guid,
+		'type' => $entity_type, 'subtype' => $entity_subtype, 'owner_guids' => $owner_guid,
 		'limit' => $limit, 'full_view' => $fullview, 'list_type_toggle' => $listtypetoggle,
 		'pagination' => $pagination,));
 }
@@ -1314,8 +1314,8 @@ function list_entities_from_metadata($meta_name, $meta_value = "", $entity_type
 	$options = array(
 		'metadata_name' => $meta_name,
 		'metadata_value' => $meta_value,
-		'types' => $entity_type,
-		'subtypes' => $entity_subtype,
+		'type' => $entity_type,
+		'subtype' => $entity_subtype,
 		'limit' => $limit,
 		'offset' => $offset,
 		'count' => TRUE,
@@ -2120,8 +2120,8 @@ $fullview = true, $listtypetoggle = false, $pagination = true, $order_by = '') {
 		'relationship' => $relationship,
 		'relationship_guid' => $relationship_guid,
 		'inverse_relationship' => $inverse_relationship,
-		'types' => $type,
-		'subtypes' => $subtype,
+		'type' => $type,
+		'subtype' => $subtype,
 		'owner_guid' => $owner_guid,
 		'order_by' => $order_by,
 		'limit' => $limit,
@@ -2566,9 +2566,9 @@ $owner_guid = "", $owner_relationship = "") {
 				'relationship' => $owner_relationship,
 				'relationship_guid' => $owner_guid[0],
 				'inverse_relationship' => FALSE,
-				'types' => 'user',
-				'subtypes' => $subtype,
-				'limit' => 9999))
+				'type' => 'user',
+				'subtype' => $subtype,
+				'limit' => false))
 			) {
 
 				$friendsarray = array();
@@ -2721,8 +2721,8 @@ function get_site_collections($site_guid, $subtype = "", $limit = 10, $offset =
 		'relationship' => 'member_of_site',
 		'relationship_guid' => $site_guid,
 		'inverse_relationship' => TRUE,
-		'types' => 'collection',
-		'subtypes' => $subtype,
+		'type' => 'collection',
+		'subtype' => $subtype,
 		'limit' => $limit,
 		'offset' => $offset
 	));
diff --git a/engine/lib/elgglib.php b/engine/lib/elgglib.php
index 540605876..74b70f9fb 100644
--- a/engine/lib/elgglib.php
+++ b/engine/lib/elgglib.php
@@ -124,11 +124,10 @@ function elgg_load_library($name) {
  * @param string $location URL to forward to browser to. Can be path relative to the network's URL.
  * @param string $reason   Short explanation for why we're forwarding
  *
- * @return False False if headers have been sent. Terminates execution if forwarding.
+ * @return false False if headers have been sent. Terminates execution if forwarding.
+ * @throws SecurityException
  */
 function forward($location = "", $reason = 'system') {
-	global $CONFIG;
-
 	if (!headers_sent()) {
 		if ($location === REFERER) {
 			$location = $_SERVER['HTTP_REFERER'];
@@ -384,7 +383,7 @@ function elgg_load_external_file($type, $name) {
 		$item->url = '';
 		$item->location = '';
 
-		$priority = $CONFIG->externals[$type]->add($item);
+		$CONFIG->externals[$type]->add($item);
 		$CONFIG->externals_map[$type][$name] = $item;
 	}
 }
@@ -528,7 +527,7 @@ function sanitise_filepath($path, $append_slash = TRUE) {
  * @param string $register Types of message: "error", "success" (default: success)
  * @param bool   $count    Count the number of messages (default: false)
  *
- * @return true|false|array Either the array of messages, or a response regarding
+ * @return bool|array Either the array of messages, or a response regarding
  *                          whether the message addition was successful.
  * @todo Clean up. Separate registering messages and retrieving them.
  */
@@ -562,7 +561,7 @@ function system_messages($message = null, $register = "success", $count = false)
 			return sizeof($_SESSION['msg'][$register]);
 		} else {
 			$count = 0;
-			foreach ($_SESSION['msg'] as $register => $submessages) {
+			foreach ($_SESSION['msg'] as $submessages) {
 				$count += sizeof($submessages);
 			}
 			return $count;
@@ -839,7 +838,7 @@ function elgg_trigger_event($event, $object_type, $object = null) {
  *
  * @param string   $hook     The name of the hook
  * @param string   $type     The type of the hook
- * @param callback $callback The name of a valid function or an array with object and method
+ * @param callable $callback The name of a valid function or an array with object and method
  * @param int      $priority The priority - 500 is default, lower numbers called first
  *
  * @return bool
@@ -885,7 +884,7 @@ function elgg_register_plugin_hook_handler($hook, $type, $callback, $priority =
  *
  * @param string   $hook        The name of the hook
  * @param string   $entity_type The name of the type of entity (eg "user", "object" etc)
- * @param callback $callback    The PHP callback to be removed
+ * @param callable $callback    The PHP callback to be removed
  *
  * @return void
  * @since 1.8.0
@@ -1060,6 +1059,7 @@ function _elgg_php_exception_handler($exception) {
  * @param array  $vars     An array that points to the active symbol table where error occurred
  *
  * @return true
+ * @throws Exception
  * @access private
  * @todo Replace error_log calls with elgg_log calls.
  */
@@ -1292,8 +1292,6 @@ function elgg_deprecated_notice($msg, $dep_version, $backtrace_level = 1) {
  * @return string The current page URL.
  */
 function current_page_url() {
-	global $CONFIG;
-
 	$url = parse_url(elgg_get_site_url());
 
 	$page = $url['scheme'] . "://";
@@ -1354,7 +1352,7 @@ function full_url() {
  * @param array $parts       Associative array of URL components like parse_url() returns
  * @param bool  $html_encode HTML Encode the url?
  *
- * @return str Full URL
+ * @return string Full URL
  * @since 1.7.0
  */
 function elgg_http_build_url(array $parts, $html_encode = TRUE) {
@@ -1385,10 +1383,10 @@ function elgg_http_build_url(array $parts, $html_encode = TRUE) {
  * add tokens to the action.  The form view automatically handles
  * tokens.
  *
- * @param str  $url         Full action URL
+ * @param string  $url         Full action URL
  * @param bool $html_encode HTML encode the url? (default: false)
  *
- * @return str URL with action tokens
+ * @return string URL with action tokens
  * @since 1.7.0
  * @link http://docs.elgg.org/Tutorials/Actions
  */
@@ -1440,17 +1438,17 @@ function elgg_http_remove_url_query_element($url, $element) {
 	}
 
 	$url_array['query'] = http_build_query($query);
-	$string = elgg_http_build_url($url_array);
+	$string = elgg_http_build_url($url_array, false);
 	return $string;
 }
 
 /**
  * Adds an element or elements to a URL's query string.
  *
- * @param str   $url      The URL
+ * @param string $url      The URL
  * @param array $elements Key/value pairs to add to the URL
  *
- * @return str The new URL with the query strings added
+ * @return string The new URL with the query strings added
  * @since 1.7.0
  */
 function elgg_http_add_url_query_elements($url, array $elements) {
@@ -1487,8 +1485,6 @@ function elgg_http_add_url_query_elements($url, array $elements) {
  * @since 1.8.0
  */
 function elgg_http_url_is_identical($url1, $url2, $ignore_params = array('offset', 'limit')) {
-	global $CONFIG;
-
 	// if the server portion is missing but it starts with / then add the url in.
 	// @todo use elgg_normalize_url()
 	if (elgg_substr($url1, 0, 1) == '/') {
@@ -1627,7 +1623,7 @@ $sort_type = SORT_LOCALE_STRING) {
 
 	$sort = array();
 
-	foreach ($array as $k => $v) {
+	foreach ($array as $v) {
 		if (isset($v[$element])) {
 			$sort[] = strtolower($v[$element]);
 		} else {
@@ -1646,7 +1642,7 @@ $sort_type = SORT_LOCALE_STRING) {
  *
  * @param string $ini_get_arg The INI setting
  *
- * @return true|false Depending on whether it's on or off
+ * @return bool Depending on whether it's on or off
  */
 function ini_get_bool($ini_get_arg) {
 	$temp = strtolower(ini_get($ini_get_arg));
@@ -1662,7 +1658,7 @@ function ini_get_bool($ini_get_arg) {
  *
  * @tip Use this for arithmetic when determining if a file can be uploaded.
  *
- * @param str $setting The php.ini setting
+ * @param string $setting The php.ini setting
  *
  * @return int
  * @since 1.7.0
@@ -1677,8 +1673,10 @@ function elgg_get_ini_setting_in_bytes($setting) {
 	switch($last) {
 		case 'g':
 			$val *= 1024;
+			// fallthrough intentional
 		case 'm':
 			$val *= 1024;
+			// fallthrough intentional
 		case 'k':
 			$val *= 1024;
 	}
@@ -1835,7 +1833,7 @@ function elgg_ajax_page_handler($page) {
  *
  * @param array $page The page array
  *
- * @return void
+ * @return bool
  * @elgg_pagehandler css
  * @access private
  */
@@ -1899,6 +1897,7 @@ function elgg_cacheable_view_page_handler($page, $type) {
 		echo $return;
 		return true;
 	}
+	return false;
 }
 
 /**
@@ -2220,7 +2219,7 @@ function elgg_init() {
  * @param array  $params empty
  *
  * @elgg_plugin_hook unit_tests system
- * @return void
+ * @return array
  * @access private
  */
 function elgg_api_test($hook, $type, $value, $params) {
@@ -2232,7 +2231,7 @@ function elgg_api_test($hook, $type, $value, $params) {
 }
 
 /**#@+
- * Controlls access levels on ElggEntity entities, metadata, and annotations.
+ * Controls access levels on ElggEntity entities, metadata, and annotations.
  *
  * @var int
  */
@@ -2266,7 +2265,7 @@ define('ELGG_ENTITIES_NO_VALUE', 0);
  * referring page.
  *
  * @see forward
- * @var unknown_type
+ * @var int -1
  */
 define('REFERRER', -1);
 
diff --git a/engine/lib/entities.php b/engine/lib/entities.php
index ce736ce05..156eec040 100644
--- a/engine/lib/entities.php
+++ b/engine/lib/entities.php
@@ -531,6 +531,7 @@ function can_write_to_container($user_guid = 0, $container_guid = 0, $type = 'al
 		// If still not approved, see if the user is a member of the group
 		// @todo this should be moved to the groups plugin/library
 		if (!$return && $user && $container instanceof ElggGroup) {
+			/* @var ElggGroup $container */
 			if ($container->isMember($user)) {
 				$return = true;
 			}
@@ -1119,16 +1120,17 @@ function _elgg_fetch_entities_from_sql($sql) {
 	// Do secondary queries and merge rows
 	if ($lookup_types) {
 		$dbprefix = elgg_get_config('dbprefix');
-	}
-	foreach ($lookup_types as $type => $guids) {
-		$set = "(" . implode(',', $guids) . ")";
-		$sql = "SELECT * FROM {$dbprefix}{$type}s_entity WHERE guid IN $set";
-		$secondary_rows = get_data($sql);
-		if ($secondary_rows) {
-			foreach ($secondary_rows as $secondary_row) {
-				$key = $guid_to_key[$secondary_row->guid];
-				// cast to arrays to merge then cast back
-				$rows[$key] = (object)array_merge((array)$rows[$key], (array)$secondary_row);
+
+		foreach ($lookup_types as $type => $guids) {
+			$set = "(" . implode(',', $guids) . ")";
+			$sql = "SELECT * FROM {$dbprefix}{$type}s_entity WHERE guid IN $set";
+			$secondary_rows = get_data($sql);
+			if ($secondary_rows) {
+				foreach ($secondary_rows as $secondary_row) {
+					$key = $guid_to_key[$secondary_row->guid];
+					// cast to arrays to merge then cast back
+					$rows[$key] = (object)array_merge((array)$rows[$key], (array)$secondary_row);
+				}
 			}
 		}
 	}
@@ -1217,13 +1219,24 @@ function elgg_get_entity_type_subtype_where_sql($table, $types, $subtypes, $pair
 			$subtype_ids = array();
 			if ($subtypes) {
 				foreach ($subtypes as $subtype) {
-					// check that the subtype is valid (with ELGG_ENTITIES_NO_VALUE being a valid subtype)
-					if (ELGG_ENTITIES_NO_VALUE === $subtype || $subtype_id = get_subtype_id($type, $subtype)) {
-						$subtype_ids[] = (ELGG_ENTITIES_NO_VALUE === $subtype) ? ELGG_ENTITIES_NO_VALUE : $subtype_id;
-					} else {
-						$valid_subtypes_count--;
-						elgg_log("Type-subtype '$type:$subtype' does not exist!", 'NOTICE');
+					// check that the subtype is valid
+					if (!$subtype && ELGG_ENTITIES_NO_VALUE === $subtype) {
+						// subtype value is 0
+						$subtype_ids[] = ELGG_ENTITIES_NO_VALUE;
+					} elseif (!$subtype) {
+						// subtype is ignored.
+						// this handles ELGG_ENTITIES_ANY_VALUE, '', and anything falsy that isn't 0
 						continue;
+					} else {
+						$subtype_id = get_subtype_id($type, $subtype);
+						
+						if ($subtype_id) {
+							$subtype_ids[] = $subtype_id;
+						} else {
+							$valid_subtypes_count--;
+							elgg_log("Type-subtype '$type:$subtype' does not exist!", 'NOTICE');
+							continue;
+						}
 					}
 				}
 
@@ -1459,11 +1472,13 @@ function elgg_list_entities(array $options = array(), $getter = 'elgg_get_entiti
  *
  * @tip Use this to generate a list of archives by month for when entities were added or updated.
  *
+ * @todo document how to pass in array for $subtype
+ *
  * @warning Months are returned in the form YYYYMM.
  *
  * @param string $type           The type of entity
  * @param string $subtype        The subtype of entity
- * @param int    $container_guid The container GUID that the entinties belong to
+ * @param int    $container_guid The container GUID that the entities belong to
  * @param int    $site_guid      The site GUID
  * @param string $order_by       Order_by SQL order by clause
  *
@@ -2413,6 +2428,7 @@ function elgg_instanceof($entity, $type = NULL, $subtype = NULL, $class = NULL)
 	$return = ($entity instanceof ElggEntity);
 
 	if ($type) {
+		/* @var ElggEntity $entity */
 		$return = $return && ($entity->getType() == $type);
 	}
 
diff --git a/engine/lib/export.php b/engine/lib/export.php
index ae9be95ce..ecc894e63 100644
--- a/engine/lib/export.php
+++ b/engine/lib/export.php
@@ -11,7 +11,7 @@
  *
  * @param mixed $object The object either an ElggEntity, ElggRelationship or ElggExtender
  *
- * @return the UUID or false
+ * @return string|false the UUID or false
  */
 function get_uuid_from_object($object) {
 	if ($object instanceof ElggEntity) {
@@ -40,8 +40,6 @@ function get_uuid_from_object($object) {
  * @return string
  */
 function guid_to_uuid($guid) {
-	global $CONFIG;
-
 	return elgg_get_site_url()  . "export/opendd/$guid/";
 }
 
@@ -53,8 +51,6 @@ function guid_to_uuid($guid) {
  * @return bool
  */
 function is_uuid_this_domain($uuid) {
-	global $CONFIG;
-
 	if (strpos($uuid, elgg_get_site_url()) === 0) {
 		return true;
 	}
@@ -67,7 +63,7 @@ function is_uuid_this_domain($uuid) {
  *
  * @param string $uuid A unique ID
  *
- * @return mixed
+ * @return ElggEntity|false
  */
 function get_entity_from_uuid($uuid) {
 	$uuid = sanitise_string($uuid);
@@ -117,18 +113,19 @@ function _process_element(ODD $odd) {
 	global $IMPORTED_DATA, $IMPORTED_OBJECT_COUNTER;
 
 	// See if anyone handles this element, return true if it is.
+	$to_be_serialised = null;
 	if ($odd) {
 		$handled = elgg_trigger_plugin_hook("import", "all", array("element" => $odd), $to_be_serialised);
-	}
 
-	// If not, then see if any of its sub elements are handled
-	if ($handled) {
-		// Increment validation counter
-		$IMPORTED_OBJECT_COUNTER ++;
-		// Return the constructed object
-		$IMPORTED_DATA[] = $handled;
+		// If not, then see if any of its sub elements are handled
+		if ($handled) {
+			// Increment validation counter
+			$IMPORTED_OBJECT_COUNTER ++;
+			// Return the constructed object
+			$IMPORTED_DATA[] = $handled;
 
-		return true;
+			return true;
+		}
 	}
 
 	return false;
@@ -167,7 +164,7 @@ function exportAsArray($guid) {
  *
  * @param int $guid The GUID.
  *
- * @return xml
+ * @return string XML
  * @see ElggEntity for an example of its usage.
  * @access private
  */
@@ -184,7 +181,7 @@ function export($guid) {
  * @param string $xml XML string
  *
  * @return bool
- * @throws Exception if there was a problem importing the data.
+ * @throws ImportException if there was a problem importing the data.
  * @access private
  */
 function import($xml) {
diff --git a/engine/lib/extender.php b/engine/lib/extender.php
index 538f601e1..8756e051b 100644
--- a/engine/lib/extender.php
+++ b/engine/lib/extender.php
@@ -86,6 +86,7 @@ function oddmetadata_to_elggextender(ElggEntity $entity, ODDMetaData $element) {
  * @return null
  * @elgg_plugin_hook_handler volatile metadata
  * @todo investigate more.
+ * @throws ImportException
  * @access private
  */
 function import_extender_plugin_hook($hook, $entity_type, $returnvalue, $params) {
@@ -94,6 +95,7 @@ function import_extender_plugin_hook($hook, $entity_type, $returnvalue, $params)
 	$tmp = NULL;
 
 	if ($element instanceof ODDMetaData) {
+		/* @var ODDMetaData $element */
 		// Recall entity
 		$entity_uuid = $element->getAttribute('entity_uuid');
 		$entity = get_entity_from_uuid($entity_uuid);
diff --git a/engine/lib/filestore.php b/engine/lib/filestore.php
index 93a127257..a3c7ba439 100644
--- a/engine/lib/filestore.php
+++ b/engine/lib/filestore.php
@@ -308,8 +308,6 @@ function get_image_resize_parameters($width, $height, $options) {
 function file_delete($guid) {
 	if ($file = get_entity($guid)) {
 		if ($file->canEdit()) {
-			$container = get_entity($file->container_guid);
-
 			$thumbnail = $file->thumbnail;
 			$smallthumb = $file->smallthumb;
 			$largethumb = $file->largethumb;
@@ -383,7 +381,7 @@ function file_get_general_file_type($mimetype) {
 /**
  * Delete a directory and all its contents
  *
- * @param str $directory Directory to delete
+ * @param string $directory Directory to delete
  *
  * @return bool
  */
@@ -500,7 +498,7 @@ function filestore_init() {
 /**
  * Unit tests for files
  *
- * @param sting  $hook   unit_test
+ * @param string  $hook   unit_test
  * @param string $type   system
  * @param mixed  $value  Array of tests
  * @param mixed  $params Params
diff --git a/engine/lib/group.php b/engine/lib/group.php
index 5a38e1ea6..624029d98 100644
--- a/engine/lib/group.php
+++ b/engine/lib/group.php
@@ -170,7 +170,7 @@ function get_group_members($group_guid, $limit = 10, $offset = 0, $site_guid = 0
 		'relationship' => 'member',
 		'relationship_guid' => $group_guid,
 		'inverse_relationship' => TRUE,
-		'types' => 'user',
+		'type' => 'user',
 		'limit' => $limit,
 		'offset' => $offset,
 		'count' => $count,
diff --git a/engine/lib/input.php b/engine/lib/input.php
index 6d1646e1a..2d9bae4dd 100644
--- a/engine/lib/input.php
+++ b/engine/lib/input.php
@@ -226,6 +226,8 @@ function elgg_clear_sticky_value($form_name, $variable) {
 /**
  * Page handler for autocomplete endpoint.
  *
+ * @todo split this into functions/objects, this is way too big
+ *
  * /livesearch?q=<query>
  *
  * Other options include:
@@ -233,6 +235,7 @@ function elgg_clear_sticky_value($form_name, $variable) {
  *     match_owner int    0/1
  *     limit       int    default is 10
  *
+ * @param array $page
  * @return string JSON string is returned and then exit
  * @access private
  */
@@ -265,10 +268,8 @@ function input_livesearch_page_handler($page) {
 	}
 
 	if (get_input('match_owner', false)) {
-		$owner_guid = $user->getGUID();
 		$owner_where = 'AND e.owner_guid = ' . $user->getGUID();
 	} else {
-		$owner_guid = null;
 		$owner_where = '';
 	}
 
@@ -289,7 +290,9 @@ function input_livesearch_page_handler($page) {
 
 				if ($entities = get_data($query)) {
 					foreach ($entities as $entity) {
+						// @todo use elgg_get_entities (don't query in a loop!)
 						$entity = get_entity($entity->guid);
+						/* @var ElggUser $entity */
 						if (!$entity) {
 							continue;
 						}
@@ -338,7 +341,9 @@ function input_livesearch_page_handler($page) {
 				";
 				if ($entities = get_data($query)) {
 					foreach ($entities as $entity) {
+						// @todo use elgg_get_entities (don't query in a loop!)
 						$entity = get_entity($entity->guid);
+						/* @var ElggGroup $entity */
 						if (!$entity) {
 							continue;
 						}
@@ -385,7 +390,9 @@ function input_livesearch_page_handler($page) {
 
 				if ($entities = get_data($query)) {
 					foreach ($entities as $entity) {
+						// @todo use elgg_get_entities (don't query in a loop!)
 						$entity = get_entity($entity->guid);
+						/* @var ElggUser $entity */
 						if (!$entity) {
 							continue;
 						}
diff --git a/engine/lib/languages.php b/engine/lib/languages.php
index 98006f7cd..17db14d98 100644
--- a/engine/lib/languages.php
+++ b/engine/lib/languages.php
@@ -77,7 +77,7 @@ function elgg_echo($message_key, $args = array(), $language = "") {
  * @param string $country_code   Standard country code (eg 'en', 'nl', 'es')
  * @param array  $language_array Formatted array of strings
  *
- * @return true|false Depending on success
+ * @return bool Depending on success
  */
 function add_translation($country_code, $language_array) {
 	global $CONFIG;
@@ -104,8 +104,6 @@ function add_translation($country_code, $language_array) {
  * @return string The language code for the site/user or "en" if not set
  */
 function get_current_language() {
-	global $CONFIG;
-
 	$language = get_language();
 
 	if (!$language) {
@@ -148,7 +146,7 @@ function _elgg_load_translations() {
 		$loaded = true;
 		$languages = array_unique(array('en', get_current_language()));
 		foreach ($languages as $language) {
-			$data = elgg_load_system_cache("$language.php");
+			$data = elgg_load_system_cache("$language.lang");
 			if ($data) {
 				add_translation($language, unserialize($data));
 			} else {
@@ -177,7 +175,7 @@ function _elgg_load_translations() {
  * @param bool   $load_all If true all languages are loaded, if
  *                         false only the current language + en are loaded
  *
- * @return void
+ * @return bool success
  */
 function register_translations($path, $load_all = false) {
 	global $CONFIG;
@@ -229,23 +227,37 @@ function register_translations($path, $load_all = false) {
 /**
  * Reload all translations from all registered paths.
  *
- * This is only called by functions which need to know all possible translations, namely the
- * statistic gathering ones.
+ * This is only called by functions which need to know all possible translations.
  *
  * @todo Better on demand loading based on language_paths array
  *
- * @return bool
+ * @return void
  */
 function reload_all_translations() {
 	global $CONFIG;
 
 	static $LANG_RELOAD_ALL_RUN;
 	if ($LANG_RELOAD_ALL_RUN) {
-		return null;
+		return;
 	}
 
-	foreach ($CONFIG->language_paths as $path => $dummy) {
-		register_translations($path, true);
+	if ($CONFIG->i18n_loaded_from_cache) {
+		$cache = elgg_get_system_cache();
+		$cache_dir = $cache->getVariable("cache_path");
+		$filenames = elgg_get_file_list($cache_dir, array(), array(), array(".lang"));
+		foreach ($filenames as $filename) {
+			if (preg_match('/([a-z]+)\.[^.]+$/', $filename, $matches)) {
+				$language = $matches[1];
+				$data = elgg_load_system_cache("$language.lang");
+				if ($data) {
+					add_translation($language, unserialize($data));
+				}
+			}
+		}
+	} else {
+		foreach ($CONFIG->language_paths as $path => $dummy) {
+			register_translations($path, true);
+		}
 	}
 
 	$LANG_RELOAD_ALL_RUN = true;
@@ -337,14 +349,3 @@ function get_missing_language_keys($language) {
 
 	return false;
 }
-
-/**
- * Initialize the language library
- * @access private
- */
-function elgg_languages_init() {
-	$lang = get_current_language();
-	elgg_register_simplecache_view("js/languages/$lang");
-}
-
-elgg_register_event_handler('init', 'system', 'elgg_languages_init');
diff --git a/engine/lib/location.php b/engine/lib/location.php
index 5b889509b..b319bb3bb 100644
--- a/engine/lib/location.php
+++ b/engine/lib/location.php
@@ -101,7 +101,7 @@ function elgg_get_entities_from_location(array $options = array()) {
 	$long_min = $long - $long_distance;
 	$long_max = $long + $long_distance;
 
-	$where = array();
+	$wheres = array();
 	$wheres[] = "lat_name.string='geo:lat'";
 	$wheres[] = "lat_value.string >= $lat_min";
 	$wheres[] = "lat_value.string <= $lat_max";
diff --git a/engine/lib/mb_wrapper.php b/engine/lib/mb_wrapper.php
index c2f5503e0..68fa69005 100644
--- a/engine/lib/mb_wrapper.php
+++ b/engine/lib/mb_wrapper.php
@@ -11,7 +11,7 @@ if (is_callable('mb_internal_encoding')) {
  * NOTE: This differs from parse_str() by returning the results
  * instead of placing them in the local scope!
  *
- * @param str $str The string
+ * @param string $str The string
  *
  * @return array
  * @since 1.7.0
diff --git a/engine/lib/metadata.php b/engine/lib/metadata.php
index f76c20f24..305e9918b 100644
--- a/engine/lib/metadata.php
+++ b/engine/lib/metadata.php
@@ -277,10 +277,18 @@ $access_id = ACCESS_PRIVATE, $allow_multiple = false) {
  *                                   all metadata that match the query instead of returning
  *                                   ElggMetadata objects.
  *
- * @return mixed
+ * @return ElggMetadata[]|mixed
  * @since 1.8.0
  */
 function elgg_get_metadata(array $options = array()) {
+
+	// @todo remove support for count shortcut - see #4393
+	// support shortcut of 'count' => true for 'metadata_calculation' => 'count'
+	if (isset($options['count']) && $options['count']) {
+		$options['metadata_calculation'] = 'count';
+		unset($options['count']);
+	}
+
 	$options['metastring_type'] = 'metadata';
 	return elgg_get_metastring_based_objects($options);
 }
@@ -302,11 +310,14 @@ function elgg_delete_metadata(array $options) {
 	if (!elgg_is_valid_options_for_batch_operation($options, 'metadata')) {
 		return false;
 	}
+	$options['metastring_type'] = 'metadata';
+	$result = elgg_batch_metastring_based_objects($options, 'elgg_batch_delete_callback', false);
 
+	// This moved last in case an object's constructor sets metadata. Currently the batch
+	// delete process has to create the entity to delete its metadata. See #5214
 	elgg_get_metadata_cache()->invalidateByOptions('delete', $options);
 
-	$options['metastring_type'] = 'metadata';
-	return elgg_batch_metastring_based_objects($options, 'elgg_batch_delete_callback', false);
+	return $result;
 }
 
 /**
@@ -412,7 +423,7 @@ function elgg_enable_metadata(array $options) {
  *
  *  metadata_owner_guids => NULL|ARR guids for metadata owners
  *
- * @return mixed If count, int. If not count, array. false on errors.
+ * @return ElggEntity[]|mixed If count, int. If not count, array. false on errors.
  * @since 1.7.0
  */
 function elgg_get_entities_from_metadata(array $options = array()) {
@@ -461,7 +472,7 @@ function elgg_get_entities_from_metadata(array $options = array()) {
  * @param array|null $order_by_metadata Array of names / direction
  * @param array|null $owner_guids       Array of owner GUIDs
  *
- * @return FALSE|array False on fail, array('joins', 'wheres')
+ * @return false|array False on fail, array('joins', 'wheres')
  * @since 1.7.0
  * @access private
  */
@@ -774,10 +785,10 @@ function string_to_tag_array($string) {
 		$ar = explode(",", $string);
 		$ar = array_map('trim', $ar);
 		$ar = array_filter($ar, 'is_not_null');
+		$ar = array_map('strip_tags', $ar);
 		return $ar;
 	}
 	return false;
-
 }
 
 /**
diff --git a/engine/lib/metastrings.php b/engine/lib/metastrings.php
index cf6dd4d98..f49b4a163 100644
--- a/engine/lib/metastrings.php
+++ b/engine/lib/metastrings.php
@@ -67,7 +67,7 @@ function get_metastring_id($string, $case_sensitive = TRUE) {
 	}
 
 	$row = FALSE;
-	$metaStrings = get_data($query, "entity_row_to_elggstar");
+	$metaStrings = get_data($query);
 	if (is_array($metaStrings)) {
 		if (sizeof($metaStrings) > 1) {
 			$ids = array();
@@ -389,11 +389,6 @@ function elgg_get_metastring_based_objects($options) {
 
 	$selects = $options['selects'];
 
-	// allow count shortcut
-	if ($options['count']) {
-		$options['metastring_calculation'] = 'count';
-	}
-
 	// For performance reasons we don't want the joins required for metadata / annotations
 	// unless we're going through one of their callbacks.
 	// this means we expect the functions passing different callbacks to pass their required joins.
@@ -520,9 +515,6 @@ function elgg_get_metastring_sql($table, $names = null, $values = null,
 
 	$db_prefix = elgg_get_config('dbprefix');
 
-	// join counter for incremental joins.
-	$i = 1;
-
 	// binary forces byte-to-byte comparision of strings, making
 	// it case- and diacritical-mark- sensitive.
 	// only supported on values.
@@ -663,9 +655,10 @@ function elgg_normalize_metastrings_options(array $options = array()) {
  *
  * @param int    $id      The object's ID
  * @param string $enabled Value to set to: yes or no
- * @param string $type    The type of table to use: metadata or anntations
+ * @param string $type    The type of table to use: metadata or annotations
  *
  * @return bool
+ * @throws InvalidParameterException
  * @since 1.8.0
  * @access private
  */
@@ -740,7 +733,7 @@ function elgg_batch_metastring_based_objects(array $options, $callback, $inc_off
  *
  * @param int    $id   The metastring-based object's ID
  * @param string $type The type: annotation or metadata
- * @return mixed
+ * @return ElggMetadata|ElggAnnotation
  *
  * @since 1.8.0
  * @access private
@@ -806,6 +799,7 @@ function elgg_delete_metastring_based_object_by_id($id, $type) {
 			}
 
 			if ($metabyname_memcache) {
+				// @todo why name_id? is that even populated?
 				$metabyname_memcache->delete("{$obj->entity_guid}:{$obj->name_id}");
 			}
 		}
diff --git a/engine/lib/navigation.php b/engine/lib/navigation.php
index 86624cd7c..118a7214c 100644
--- a/engine/lib/navigation.php
+++ b/engine/lib/navigation.php
@@ -126,6 +126,7 @@ function elgg_unregister_menu_item($menu_name, $item_name) {
 	}
 
 	foreach ($CONFIG->menus[$menu_name] as $index => $menu_object) {
+		/* @var ElggMenuItem $menu_object */
 		if ($menu_object->getName() == $item_name) {
 			unset($CONFIG->menus[$menu_name][$index]);
 			return true;
@@ -151,7 +152,8 @@ function elgg_is_menu_item_registered($menu_name, $item_name) {
 		return false;
 	}
 
-	foreach ($CONFIG->menus[$menu_name] as $index => $menu_object) {
+	foreach ($CONFIG->menus[$menu_name] as $menu_object) {
+		/* @var ElggMenuItem $menu_object */
 		if ($menu_object->getName() == $item_name) {
 			return true;
 		}
@@ -311,8 +313,8 @@ function elgg_site_menu_setup($hook, $type, $return, $params) {
 	
 	// check if we have anything selected
 	$selected = false;
-	foreach ($return as $section_name => $section) {
-		foreach ($section as $key => $item) {
+	foreach ($return as $section) {
+		foreach ($section as $item) {
 			if ($item->getSelected()) {
 				$selected = true;
 				break 2;
@@ -345,6 +347,7 @@ function elgg_site_menu_setup($hook, $type, $return, $params) {
 function elgg_river_menu_setup($hook, $type, $return, $params) {
 	if (elgg_is_logged_in()) {
 		$item = $params['item'];
+		/* @var ElggRiverItem $item */
 		$object = $item->getObjectEntity();
 		// comments and non-objects cannot be commented on or liked
 		if (!elgg_in_context('widgets') && $item->annotation_id == 0) {
@@ -388,6 +391,7 @@ function elgg_entity_menu_setup($hook, $type, $return, $params) {
 	}
 	
 	$entity = $params['entity'];
+	/* @var ElggEntity $entity */
 	$handler = elgg_extract('handler', $params, false);
 
 	// access
@@ -433,6 +437,7 @@ function elgg_entity_menu_setup($hook, $type, $return, $params) {
 function elgg_widget_menu_setup($hook, $type, $return, $params) {
 
 	$widget = $params['entity'];
+	/* @var ElggWidget $widget */
 	$show_edit = elgg_extract('show_edit', $params, true);
 
 	$collapse = array(
@@ -481,6 +486,7 @@ function elgg_widget_menu_setup($hook, $type, $return, $params) {
  */
 function elgg_annotation_menu_setup($hook, $type, $return, $params) {
 	$annotation = $params['annotation'];
+	/* @var ElggAnnotation $annotation */
 
 	if ($annotation->name == 'generic_comment' && $annotation->canEdit()) {
 		$url = elgg_http_add_url_query_elements('action/comments/delete', array(
diff --git a/engine/lib/notification.php b/engine/lib/notification.php
index 9e3c075a8..b6399b3c6 100644
--- a/engine/lib/notification.php
+++ b/engine/lib/notification.php
@@ -86,7 +86,7 @@ function unregister_notification_handler($method) {
  * @throws NotificationException
  */
 function notify_user($to, $from, $subject, $message, array $params = NULL, $methods_override = "") {
-	global $NOTIFICATION_HANDLERS, $CONFIG;
+	global $NOTIFICATION_HANDLERS;
 
 	// Sanitise
 	if (!is_array($to)) {
@@ -174,7 +174,8 @@ function get_user_notification_settings($user_guid = 0) {
 		$user_guid = elgg_get_logged_in_user_guid();
 	}
 
-	// @todo: holy crap, really?
+	// @todo: there should be a better way now that metadata is cached. E.g. just query for MD names, then
+	// query user object directly
 	$all_metadata = elgg_get_metadata(array(
 		'guid' => $user_guid,
 		'limit' => 0
@@ -237,6 +238,7 @@ function set_user_notification_setting($user_guid, $method, $value) {
  * @param array      $params  Optional parameters (none taken in this instance)
  *
  * @return bool
+ * @throws NotificationException
  * @access private
  */
 function email_notify_handler(ElggEntity $from, ElggUser $to, $subject, $message,
@@ -263,7 +265,7 @@ array $params = NULL) {
 	$to = $to->email;
 
 	// From
-	$site = get_entity($CONFIG->site_guid);
+	$site = elgg_get_site_entity();
 	// If there's an email address, use it - but only if its not from a user.
 	if (!($from instanceof ElggUser) && $from->email) {
 		$from = $from->email;
@@ -288,6 +290,7 @@ array $params = NULL) {
  * @param array  $params  Optional parameters (none used in this function)
  *
  * @return bool
+ * @throws NotificationException
  * @since 1.7.2
  */
 function elgg_send_email($from, $to, $subject, $body, array $params = NULL) {
@@ -344,6 +347,8 @@ function elgg_send_email($from, $to, $subject, $body, array $params = NULL) {
 
 	// Sanitise subject by stripping line endings
 	$subject = preg_replace("/(\r\n|\r|\n)/", " ", $subject);
+	// this is because Elgg encodes everything and matches what is done with body
+	$subject = html_entity_decode($subject, ENT_COMPAT, 'UTF-8'); // Decode any html entities
 	if (is_callable('mb_encode_mimeheader')) {
 		$subject = mb_encode_mimeheader($subject, "UTF-8", "B");
 	}
@@ -422,7 +427,7 @@ function register_notification_object($entity_type, $object_subtype, $language_n
  * @param int $user_guid   The GUID of the user who wants to follow a user's content
  * @param int $author_guid The GUID of the user whose content the user wants to follow
  *
- * @return true|false Depending on success
+ * @return bool Depending on success
  */
 function register_notification_interest($user_guid, $author_guid) {
 	return add_entity_relationship($user_guid, 'notify', $author_guid);
@@ -434,7 +439,7 @@ function register_notification_interest($user_guid, $author_guid) {
  * @param int $user_guid   The GUID of the user who is following a user's content
  * @param int $author_guid The GUID of the user whose content the user wants to unfollow
  *
- * @return true|false Depending on success
+ * @return bool Depending on success
  */
 function remove_notification_interest($user_guid, $author_guid) {
 	return remove_entity_relationship($user_guid, 'notify', $author_guid);
@@ -450,12 +455,13 @@ function remove_notification_interest($user_guid, $author_guid) {
  * @param string $object_type mixed
  * @param mixed  $object      The object created
  *
- * @return void
+ * @return bool
  * @access private
  */
 function object_notifications($event, $object_type, $object) {
 	// We only want to trigger notification events for ElggEntities
 	if ($object instanceof ElggEntity) {
+		/* @var ElggEntity $object */
 
 		// Get config data
 		global $CONFIG, $SESSION, $NOTIFICATION_HANDLERS;
@@ -492,9 +498,10 @@ function object_notifications($event, $object_type, $object) {
 					'relationship' => 'notify' . $method,
 					'relationship_guid' => $object->container_guid,
 					'inverse_relationship' => TRUE,
-					'types' => 'user',
-					'limit' => 99999
+					'type' => 'user',
+					'limit' => false
 				));
+				/* @var ElggUser[] $interested_users */
 
 				if ($interested_users && is_array($interested_users)) {
 					foreach ($interested_users as $user) {
diff --git a/engine/lib/objects.php b/engine/lib/objects.php
index e5e8f67c4..ff3cc733f 100644
--- a/engine/lib/objects.php
+++ b/engine/lib/objects.php
@@ -93,16 +93,16 @@ function get_object_sites($object_guid, $limit = 10, $offset = 0) {
 	return elgg_get_entities_from_relationship(array(
 		'relationship' => 'member_of_site',
 		'relationship_guid' => $object_guid,
-		'types' => 'site',
+		'type' => 'site',
 		'limit' => $limit,
-		'offset' => $offset
+		'offset' => $offset,
 	));
 }
 
 /**
  * Runs unit tests for ElggObject
  *
- * @param sting  $hook   unit_test
+ * @param string  $hook   unit_test
  * @param string $type   system
  * @param mixed  $value  Array of tests
  * @param mixed  $params Params
diff --git a/engine/lib/output.php b/engine/lib/output.php
index 9295f2173..da8e1ab86 100644
--- a/engine/lib/output.php
+++ b/engine/lib/output.php
@@ -12,7 +12,7 @@
  *
  * @param string $text The input string
  *
- * @return string The output stirng with formatted links
+ * @return string The output string with formatted links
  **/
 function parse_urls($text) {
 	// @todo this causes problems with <attr = "val">
@@ -224,7 +224,6 @@ function elgg_normalize_url($url) {
 	$php_5_3_0_to_5_3_2 = version_compare(PHP_VERSION, '5.3.0', '>=') &&
 			version_compare(PHP_VERSION, '5.3.3', '<');
 
-	$validated = false;
 	if ($php_5_2_13_and_below || $php_5_3_0_to_5_3_2) {
 		$tmp_address = str_replace("-", "", $url);
 		$validated = filter_var($tmp_address, FILTER_VALIDATE_URL);
@@ -421,7 +420,7 @@ function _elgg_html_decode($string) {
 /**
  * Unit tests for Output
  *
- * @param sting  $hook   unit_test
+ * @param string  $hook   unit_test
  * @param string $type   system
  * @param mixed  $value  Array of tests
  * @param mixed  $params Params
diff --git a/engine/lib/pageowner.php b/engine/lib/pageowner.php
index 94765feee..7fd79e68a 100644
--- a/engine/lib/pageowner.php
+++ b/engine/lib/pageowner.php
@@ -39,7 +39,7 @@ function elgg_get_page_owner_guid($guid = 0) {
  *
  * @note Access is disabled when getting the page owner entity.
  *
- * @return ElggEntity|false The current page owner or false if none.
+ * @return ElggUser|ElggGroup|false The current page owner or false if none.
  *
  * @since 1.8.0
  */
@@ -113,6 +113,7 @@ function default_page_owner_handler($hook, $entity_type, $returnvalue, $params)
 		}
 
 		if ($user = get_user_by_username($username)) {
+			elgg_set_ignore_access($ia);
 			return $user->getGUID();
 		}
 	}
@@ -140,7 +141,7 @@ function default_page_owner_handler($hook, $entity_type, $returnvalue, $params)
 			switch ($segments[1]) {
 				case 'owner':
 				case 'friends':
-					$user = get_user_by_username($segments[2]);
+					$user = get_user_by_username(urldecode($segments[2]));
 					if ($user) {
 						elgg_set_ignore_access($ia);
 						return $user->getGUID();
diff --git a/engine/lib/plugins.php b/engine/lib/plugins.php
index 94aff277e..f281b1416 100644
--- a/engine/lib/plugins.php
+++ b/engine/lib/plugins.php
@@ -91,7 +91,9 @@ function elgg_get_plugin_ids_in_dir($dir = null) {
  * @access private
  */
 function elgg_generate_plugin_entities() {
+	// @todo $site unused, can remove?
 	$site = get_config('site');
+
 	$dir = elgg_get_plugins_path();
 	$db_prefix = elgg_get_config('dbprefix');
 
@@ -107,6 +109,7 @@ function elgg_generate_plugin_entities() {
 	$old_access = access_get_show_hidden_status();
 	access_show_hidden_entities(true);
 	$known_plugins = elgg_get_entities_from_relationship($options);
+	/* @var ElggPlugin[] $known_plugins */
 
 	if (!$known_plugins) {
 		$known_plugins = array();
@@ -138,7 +141,7 @@ function elgg_generate_plugin_entities() {
 			$index = $id_map[$plugin_id];
 			$plugin = $known_plugins[$index];
 			// was this plugin deleted and its entity disabled?
-			if ($plugin->enabled != 'yes') {
+			if (!$plugin->isEnabled()) {
 				$plugin->enable();
 				$plugin->deactivate();
 				$plugin->setPriority('last');
@@ -192,7 +195,7 @@ function _elgg_cache_plugin_by_id(ElggPlugin $plugin) {
  * Returns an ElggPlugin object with the path $path.
  *
  * @param string $plugin_id The id (dir name) of the plugin. NOT the guid.
- * @return mixed ElggPlugin or false.
+ * @return ElggPlugin|false
  * @since 1.8.0
  */
 function elgg_get_plugin_from_id($plugin_id) {
@@ -260,6 +263,8 @@ function elgg_get_max_plugin_priority() {
 	$data = get_data($q);
 	if ($data) {
 		$max = $data[0]->max;
+	} else {
+		$max = 1;
 	}
 
 	// can't have a priority of 0.
@@ -306,8 +311,6 @@ function elgg_is_active_plugin($plugin_id, $site_guid = null) {
  * @access private
  */
 function elgg_load_plugins() {
-	global $CONFIG;
-
 	$plugins_path = elgg_get_plugins_path();
 	$start_flags =	ELGG_PLUGIN_INCLUDE_START
 					| ELGG_PLUGIN_REGISTER_VIEWS
@@ -360,7 +363,7 @@ function elgg_load_plugins() {
  *
  * @param string $status      The status of the plugins. active, inactive, or all.
  * @param mixed  $site_guid   Optional site guid
- * @return array
+ * @return ElggPlugin[]
  * @since 1.8.0
  * @access private
  */
@@ -441,6 +444,7 @@ function elgg_set_plugin_priorities(array $order) {
 	// though we do start with 1
 	$order = array_values($order);
 
+	$missing_plugins = array();
 	foreach ($plugins as $plugin) {
 		$plugin_id = $plugin->getID();
 
@@ -639,19 +643,18 @@ function elgg_get_plugins_provides($type = null, $name = null) {
  * @access private
  */
 function elgg_check_plugins_provides($type, $name, $version = null, $comparison = 'ge') {
-	if (!$provided = elgg_get_plugins_provides($type, $name)) {
+	$provided = elgg_get_plugins_provides($type, $name);
+	if (!$provided) {
 		return array(
 			'status' => false,
 			'version' => ''
 		);
 	}
 
-	if ($provided) {
-		if ($version) {
-			$status = version_compare($provided['version'], $version, $comparison);
-		} else {
-			$status = true;
-		}
+	if ($version) {
+		$status = version_compare($provided['version'], $version, $comparison);
+	} else {
+		$status = true;
 	}
 
 	return array(
@@ -861,9 +864,9 @@ function elgg_set_plugin_user_setting($name, $value, $user_guid = null, $plugin_
 /**
  * Unsets a user-specific plugin setting
  *
- * @param str $name      Name of the setting
+ * @param string $name      Name of the setting
  * @param int $user_guid Defaults to logged in user
- * @param str $plugin_id Defaults to contextual plugin name
+ * @param string $plugin_id Defaults to contextual plugin name
  *
  * @return bool
  * @since 1.8.0
@@ -1087,7 +1090,7 @@ function plugin_run_once() {
 /**
  * Runs unit tests for the entity objects.
  *
- * @param sting  $hook   unit_test
+ * @param string  $hook   unit_test
  * @param string $type   system
  * @param mixed  $value  Array of tests
  * @param mixed  $params Params
diff --git a/engine/lib/relationships.php b/engine/lib/relationships.php
index 01654b1ce..fe0b8364d 100644
--- a/engine/lib/relationships.php
+++ b/engine/lib/relationships.php
@@ -12,7 +12,7 @@
  *
  * @param stdClass $row Database row from the relationship table
  *
- * @return stdClass or ElggMetadata
+ * @return ElggRelationship|stdClass
  * @access private
  */
 function row_to_elggrelationship($row) {
@@ -28,7 +28,7 @@ function row_to_elggrelationship($row) {
  *
  * @param int $id The ID of a relationship
  *
- * @return mixed
+ * @return ElggRelationship|false
  */
 function get_relationship($id) {
 	global $CONFIG;
@@ -109,7 +109,7 @@ function add_entity_relationship($guid_one, $relationship, $guid_two) {
  * @param string $relationship The type of relationship
  * @param int    $guid_two     The GUID of the entity the relationship is with
  *
- * @return object|false Depending on success
+ * @return ElggRelationship|false Depending on success
  */
 function check_entity_relationship($guid_one, $relationship, $guid_two) {
 	global $CONFIG;
@@ -123,7 +123,7 @@ function check_entity_relationship($guid_one, $relationship, $guid_two) {
 			AND relationship='$relationship'
 			AND guid_two=$guid_two limit 1";
 
-	$row = get_data_row($query);
+	$row = row_to_elggrelationship(get_data_row($query));
 	if ($row) {
 		return $row;
 	}
@@ -220,7 +220,7 @@ function remove_entity_relationships($guid_one, $relationship = "", $inverse = f
  * @param int  $guid                 The GUID of the relationship owner
  * @param bool $inverse_relationship Inverse relationship owners?
  *
- * @return mixed
+ * @return ElggRelationship[]
  */
 function get_entity_relationships($guid, $inverse_relationship = FALSE) {
 	global $CONFIG;
@@ -259,7 +259,7 @@ function get_entity_relationships($guid, $inverse_relationship = FALSE) {
  *
  * 	inverse_relationship => BOOL Inverse the relationship
  *
- * @return mixed If count, int. If not count, array. false on errors.
+ * @return ElggEntity[]|mixed If count, int. If not count, array. false on errors.
  * @since 1.7.0
  */
 function elgg_get_entities_from_relationship($options) {
@@ -316,7 +316,7 @@ function elgg_get_entities_from_relationship($options) {
  *                                     Provide in table.column format.
  * @param string $relationship         Relationship string
  * @param int    $relationship_guid    Entity guid to check
- * @param string $inverse_relationship Inverse relationship check?
+ * @param bool $inverse_relationship Inverse relationship check?
  *
  * @return mixed
  * @since 1.7.0
@@ -381,7 +381,7 @@ function elgg_list_entities_from_relationship(array $options = array()) {
  *
  * @param array $options An options array compatible with
  *                       elgg_get_entities_from_relationship()
- * @return mixed int If count, int. If not count, array. false on errors.
+ * @return ElggEntity[]|mixed int If count, int. If not count, array. false on errors.
  * @since 1.8.0
  */
 function elgg_get_entities_from_relationship_count(array $options = array()) {
@@ -398,7 +398,7 @@ function elgg_get_entities_from_relationship_count(array $options = array()) {
  *
  * @param array $options Options array
  *
- * @return array
+ * @return string
  * @since 1.8.0
  */
 function elgg_list_entities_from_relationship_count($options) {
@@ -499,7 +499,7 @@ function already_attached($guid_one, $guid_two) {
  * @param int    $guid Entity GUID
  * @param string $type The type of object to return e.g. 'file', 'friend_of' etc
  *
- * @return an array of objects
+ * @return ElggEntity[]
  * @access private
  */
 function get_attachments($guid, $type = "") {
@@ -507,7 +507,7 @@ function get_attachments($guid, $type = "") {
 					'relationship' => 'attached',
 					'relationship_guid' => $guid,
 					'inverse_relationship' => false,
-					'types' => $type,
+					'type' => $type,
 					'subtypes' => '',
 					'owner_guid' => 0,
 					'order_by' => 'time_created desc',
@@ -571,9 +571,8 @@ function import_relationship_plugin_hook($hook, $entity_type, $returnvalue, $par
 	if ($element instanceof ODDRelationship) {
 		$tmp = new ElggRelationship();
 		$tmp->import($element);
-
-		return $tmp;
 	}
+	return $tmp;
 }
 
 /**
@@ -586,11 +585,10 @@ function import_relationship_plugin_hook($hook, $entity_type, $returnvalue, $par
  *
  * @elgg_event_handler export all
  * @return mixed
+ * @throws InvalidParameterException
  * @access private
  */
 function export_relationship_plugin_hook($hook, $entity_type, $returnvalue, $params) {
-	global $CONFIG;
-
 	// Sanity check values
 	if ((!is_array($params)) && (!isset($params['guid']))) {
 		throw new InvalidParameterException(elgg_echo('InvalidParameterException:GUIDNotForExport'));
@@ -624,9 +622,9 @@ function export_relationship_plugin_hook($hook, $entity_type, $returnvalue, $par
  * @access private
  */
 function relationship_notification_hook($event, $type, $object) {
-
+	/* @var ElggRelationship $object */
 	$user_one = get_entity($object->guid_one);
-	$user_two = get_entity($object->guid_two);
+	/* @var ElggUser $user_one */
 
 	return notify_user($object->guid_two,
 			$object->guid_one,
diff --git a/engine/lib/river.php b/engine/lib/river.php
index 33f34360e..f2ec1e101 100644
--- a/engine/lib/river.php
+++ b/engine/lib/river.php
@@ -500,6 +500,7 @@ function elgg_get_river_type_subtype_where_sql($table, $types, $subtypes, $pairs
 		return '';
 	}
 
+	$wheres = array();
 	$types_wheres = array();
 	$subtypes_wheres = array();
 
@@ -644,7 +645,7 @@ function update_river_access_by_object($object_guid, $access_id) {
 }
 
 /**
- * Page handler for activiy
+ * Page handler for activity
  *
  * @param array $page
  * @return bool
@@ -663,10 +664,6 @@ function elgg_river_page_handler($page) {
 	}
 	set_input('page_type', $page_type);
 
-	// content filter code here
-	$entity_type = '';
-	$entity_subtype = '';
-
 	require_once("{$CONFIG->path}pages/river.php");
 	return true;
 }
diff --git a/engine/lib/sessions.php b/engine/lib/sessions.php
index 72ca0a1c2..a34c2045b 100644
--- a/engine/lib/sessions.php
+++ b/engine/lib/sessions.php
@@ -286,8 +286,6 @@ function check_rate_limit_exceeded($user_guid) {
  * @throws LoginException
  */
 function login(ElggUser $user, $persistent = false) {
-	global $CONFIG;
-
 	// User is banned, return false.
 	if ($user->isBanned()) {
 		throw new LoginException(elgg_echo('LoginException:BannedUser'));
@@ -334,8 +332,6 @@ function login(ElggUser $user, $persistent = false) {
  * @return bool
  */
 function logout() {
-	global $CONFIG;
-
 	if (isset($_SESSION['user'])) {
 		if (!elgg_trigger_event('logout', 'user', $_SESSION['user'])) {
 			return false;
@@ -616,10 +612,8 @@ function _elgg_session_destroy($id) {
 		global $sess_save_path;
 
 		$sess_file = "$sess_save_path/sess_$id";
-		return(@unlink($sess_file));
+		return @unlink($sess_file);
 	}
-
-	return false;
 }
 
 /**
diff --git a/engine/lib/sites.php b/engine/lib/sites.php
index d9eb2d25e..3de0eccc2 100644
--- a/engine/lib/sites.php
+++ b/engine/lib/sites.php
@@ -26,7 +26,7 @@ function elgg_get_site_entity($site_guid = 0) {
 		$site = get_entity($site_guid);
 	}
 	
-	if($site instanceof ElggSite){
+	if ($site instanceof ElggSite) {
 		$result = $site;
 	}
 
@@ -118,8 +118,6 @@ function create_site_entity($guid, $name, $description, $url) {
  * @return bool
  */
 function add_site_user($site_guid, $user_guid) {
-	global $CONFIG;
-
 	$site_guid = (int)$site_guid;
 	$user_guid = (int)$user_guid;
 
@@ -150,8 +148,6 @@ function remove_site_user($site_guid, $user_guid) {
  * @return mixed
  */
 function add_site_object($site_guid, $object_guid) {
-	global $CONFIG;
-
 	$site_guid = (int)$site_guid;
 	$object_guid = (int)$object_guid;
 
@@ -192,8 +188,8 @@ function get_site_objects($site_guid, $subtype = "", $limit = 10, $offset = 0) {
 		'relationship' => 'member_of_site',
 		'relationship_guid' => $site_guid,
 		'inverse_relationship' => TRUE,
-		'types' => 'object',
-		'subtypes' => $subtype,
+		'type' => 'object',
+		'subtype' => $subtype,
 		'limit' => $limit,
 		'offset' => $offset
 	));
@@ -242,7 +238,7 @@ function get_site_domain($guid) {
 /**
  * Unit tests for sites
  *
- * @param sting  $hook   unit_test
+ * @param string $hook   unit_test
  * @param string $type   system
  * @param mixed  $value  Array of tests
  * @param mixed  $params Params
diff --git a/engine/lib/statistics.php b/engine/lib/statistics.php
index 5ee640549..0c9a3c945 100644
--- a/engine/lib/statistics.php
+++ b/engine/lib/statistics.php
@@ -101,9 +101,10 @@ function get_online_users() {
 	if ($objects) {
 		return elgg_view_entity_list($objects, array(
 			'count' => $count,
-			'limit' => 10
+			'limit' => 10,
 		));
 	}
+	return '';
 }
 
 /**
diff --git a/engine/lib/system_log.php b/engine/lib/system_log.php
index 53fa24557..5a153afb2 100644
--- a/engine/lib/system_log.php
+++ b/engine/lib/system_log.php
@@ -10,6 +10,8 @@
 /**
  * Retrieve the system log based on a number of parameters.
  *
+ * @todo too many args, and the first arg is too confusing
+ *
  * @param int|array $by_user    The guid(s) of the user(s) who initiated the event.
  *                              Use 0 for unowned entries. Anything else falsey means anyone.
  * @param string    $event      The event you are searching on.
@@ -22,12 +24,12 @@
  * @param int       $timebefore Lower time limit
  * @param int       $timeafter  Upper time limit
  * @param int       $object_id  GUID of an object
- * @param str       $ip_address The IP address.
+ * @param string    $ip_address The IP address.
  * @return mixed
  */
-function get_system_log($by_user = "", $event = "", $class = "", $type = "", $subtype = "",
-$limit = 10, $offset = 0, $count = false, $timebefore = 0, $timeafter = 0, $object_id = 0,
-$ip_address = false) {
+function get_system_log($by_user = "", $event = "", $class = "", $type = "", $subtype = "", $limit = 10,
+						$offset = 0, $count = false, $timebefore = 0, $timeafter = 0, $object_id = 0,
+						$ip_address = "") {
 
 	global $CONFIG;
 
@@ -166,6 +168,7 @@ function system_log($object, $event) {
 
 	if ($object instanceof Loggable) {
 
+		/* @var ElggEntity|ElggExtender $object */
 		if (datalist_get('version') < 2012012000) {
 			// this is a site that doesn't have the ip_address column yet
 			return;
diff --git a/engine/lib/tags.php b/engine/lib/tags.php
index a0887d0f3..586a9b9e4 100644
--- a/engine/lib/tags.php
+++ b/engine/lib/tags.php
@@ -48,7 +48,7 @@ function calculate_tag_size($min, $max, $number_of_tags, $buckets = 6) {
  * @param array $tags    The array of tags.
  * @param int   $buckets The number of buckets
  *
- * @return An associated array of tags with a weighting, this can then be mapped to a display class.
+ * @return array An associated array of tags with a weighting, this can then be mapped to a display class.
  * @access private
  */
 function generate_tag_cloud(array $tags, $buckets = 6) {
@@ -114,8 +114,8 @@ function generate_tag_cloud(array $tags, $buckets = 6) {
  *
  * 	joins => array() Additional joins
  *
- * @return 	false/array - if no tags or error, false
- * 			otherwise, array of objects with ->tag and ->total values
+ * @return 	object[]|false If no tags or error, false
+ * 						   otherwise, array of objects with ->tag and ->total values
  * @since 1.7.1
  */
 function elgg_get_tags(array $options = array()) {
@@ -172,6 +172,7 @@ function elgg_get_tags(array $options = array()) {
 	// catch for tags that were spaces
 	$wheres[] = "msv.string != ''";
 
+	$sanitised_tags = array();
 	foreach ($options['tag_names'] as $tag) {
 		$sanitised_tags[] = '"' . sanitise_string($tag) . '"';
 	}
diff --git a/engine/lib/upgrade.php b/engine/lib/upgrade.php
index f4f4b16f5..d684af862 100644
--- a/engine/lib/upgrade.php
+++ b/engine/lib/upgrade.php
@@ -17,8 +17,9 @@
  * @access private
  */
 function upgrade_code($version, $quiet = FALSE) {
+	// do not remove - upgrade scripts depend on this
 	global $CONFIG;
-
+	
 	$version = (int) $version;
 	$upgrade_path = elgg_get_config('path') . 'engine/lib/upgrades/';
 	$processed_upgrades = elgg_get_processed_upgrades();
@@ -291,7 +292,6 @@ function elgg_upgrade_bootstrap_17_to_18() {
 		'2011010101.php',
 	);
 
-	$upgrades_17 = array();
 	$upgrade_files = elgg_get_upgrade_files();
 	$processed_upgrades = array();
 
@@ -360,6 +360,7 @@ function _elgg_upgrade_is_locked() {
 	
 	// Invalidate query cache
 	if ($DB_QUERY_CACHE) {
+		/* @var ElggStaticVariableCache $DB_QUERY_CACHE */
 		$DB_QUERY_CACHE->clear();
 		elgg_log("Query cache invalidated", 'NOTICE');
 	}
diff --git a/engine/lib/upgrades/2013030600-1.8.13-update_user_location-8999eb8bf1bdd9a3.php b/engine/lib/upgrades/2013030600-1.8.13-update_user_location-8999eb8bf1bdd9a3.php
new file mode 100644
index 000000000..b38eb5100
--- /dev/null
+++ b/engine/lib/upgrades/2013030600-1.8.13-update_user_location-8999eb8bf1bdd9a3.php
@@ -0,0 +1,26 @@
+<?php
+/**
+ * Elgg 1.8.14 upgrade 2013030600
+ * update_user_location
+ *
+ * Before Elgg 1.8, a location like "London, England" would be stored as an array.
+ * This script turns that back into a string.
+ */
+
+global $DB_QUERY_CACHE;
+
+$ia = elgg_set_ignore_access(true);
+$options = array(
+	'type' => 'user',
+	'limit' => 0,
+);
+$batch = new ElggBatch('elgg_get_entities', $options);
+
+foreach ($batch as $entity) {
+	$DB_QUERY_CACHE = array();
+	
+	if (is_array($entity->location)) {
+		$entity->location = implode(', ', $entity->location);
+	}
+}
+elgg_set_ignore_access($ia);
diff --git a/engine/lib/upgrades/create_upgrade.php b/engine/lib/upgrades/create_upgrade.php
index 3652e18a2..b34f31b7e 100644
--- a/engine/lib/upgrades/create_upgrade.php
+++ b/engine/lib/upgrades/create_upgrade.php
@@ -93,7 +93,7 @@ if (!$h) {
 	die("Could not open file $upgrade_file");
 }
 
-if (!fputs($h, $upgrade_code)) {
+if (!fwrite($h, $upgrade_code)) {
 	die("Could not write to $upgrade_file");
 } else {
 	elgg_set_version_dot_php_version($upgrade_version);
@@ -128,8 +128,9 @@ function elgg_set_version_dot_php_version($version) {
 
 	rewind($h);
 
-	fputs($h, $out);
+	fwrite($h, $out);
 	fclose($h);
+	return true;
 }
 
 /**
diff --git a/engine/lib/user_settings.php b/engine/lib/user_settings.php
index e4069fb53..3466c25f9 100644
--- a/engine/lib/user_settings.php
+++ b/engine/lib/user_settings.php
@@ -265,9 +265,9 @@ function elgg_set_user_default_access() {
  * @access private
  */
 function usersettings_pagesetup() {
-	if (elgg_get_context() == "settings") {
-		$user = elgg_get_page_owner_entity();
+	$user = elgg_get_page_owner_entity();
 
+	if ($user && elgg_get_context() == "settings") {
 		$params = array(
 			'name' => '1_account',
 			'text' => elgg_echo('usersettings:user:opt:linktext'),
@@ -332,6 +332,7 @@ function usersettings_page_handler($page) {
 		require $path;
 		return true;
 	}
+	return false;
 }
 
 /**
diff --git a/engine/lib/users.php b/engine/lib/users.php
index 95ef9d176..4a585c07f 100644
--- a/engine/lib/users.php
+++ b/engine/lib/users.php
@@ -290,7 +290,7 @@ function remove_user_admin($user_guid) {
  * @param int $limit     Number of results to return
  * @param int $offset    Any indexing offset
  *
- * @return false|array On success, an array of ElggSites
+ * @return ElggSite[]|false On success, an array of ElggSites
  */
 function get_user_sites($user_guid, $limit = 10, $offset = 0) {
 	$user_guid = (int)$user_guid;
@@ -302,7 +302,7 @@ function get_user_sites($user_guid, $limit = 10, $offset = 0) {
 		'relationship' => 'member_of_site',
 		'relationship_guid' => $user_guid,
 		'inverse_relationship' => FALSE,
-		'types' => 'site',
+		'type' => 'site',
 		'limit' => $limit,
 		'offset' => $offset,
 	));
@@ -343,8 +343,6 @@ function user_add_friend($user_guid, $friend_guid) {
  * @return bool Depending on success
  */
 function user_remove_friend($user_guid, $friend_guid) {
-	global $CONFIG;
-
 	$user_guid = (int) $user_guid;
 	$friend_guid = (int) $friend_guid;
 
@@ -379,7 +377,7 @@ function user_is_friend($user_guid, $friend_guid) {
  * @param int    $limit     Number of results to return (default 10)
  * @param int    $offset    Indexing offset, if any
  *
- * @return false|array Either an array of ElggUsers or false, depending on success
+ * @return ElggUser[]|false Either an array of ElggUsers or false, depending on success
  */
 function get_user_friends($user_guid, $subtype = ELGG_ENTITIES_ANY_VALUE, $limit = 10,
 $offset = 0) {
@@ -387,8 +385,8 @@ $offset = 0) {
 	return elgg_get_entities_from_relationship(array(
 		'relationship' => 'friend',
 		'relationship_guid' => $user_guid,
-		'types' => 'user',
-		'subtypes' => $subtype,
+		'type' => 'user',
+		'subtype' => $subtype,
 		'limit' => $limit,
 		'offset' => $offset
 	));
@@ -402,7 +400,7 @@ $offset = 0) {
  * @param int    $limit     Number of results to return (default 10)
  * @param int    $offset    Indexing offset, if any
  *
- * @return false|array Either an array of ElggUsers or false, depending on success
+ * @return ElggUser[]|false Either an array of ElggUsers or false, depending on success
  */
 function get_user_friends_of($user_guid, $subtype = ELGG_ENTITIES_ANY_VALUE, $limit = 10,
 $offset = 0) {
@@ -411,8 +409,8 @@ $offset = 0) {
 		'relationship' => 'friend',
 		'relationship_guid' => $user_guid,
 		'inverse_relationship' => TRUE,
-		'types' => 'user',
-		'subtypes' => $subtype,
+		'type' => 'user',
+		'subtype' => $subtype,
 		'limit' => $limit,
 		'offset' => $offset
 	));
@@ -428,7 +426,7 @@ $offset = 0) {
  * @param int    $timelower The earliest time the entity can have been created. Default: all
  * @param int    $timeupper The latest time the entity can have been created. Default: all
  *
- * @return false|array An array of ElggObjects or false, depending on success
+ * @return ElggObject[]|false An array of ElggObjects or false, depending on success
  */
 function get_user_friends_objects($user_guid, $subtype = ELGG_ENTITIES_ANY_VALUE, $limit = 10,
 $offset = 0, $timelower = 0, $timeupper = 0) {
@@ -560,7 +558,7 @@ function get_user_by_username($username) {
 
 	// Caching
 	if ((isset($USERNAME_TO_GUID_MAP_CACHE[$username]))
-	&& (retrieve_cached_entity($USERNAME_TO_GUID_MAP_CACHE[$username]))) {
+			&& (retrieve_cached_entity($USERNAME_TO_GUID_MAP_CACHE[$username]))) {
 		return retrieve_cached_entity($USERNAME_TO_GUID_MAP_CACHE[$username]);
 	}
 
@@ -675,25 +673,22 @@ function find_active_users($seconds = 600, $limit = 10, $offset = 0, $count = fa
  * @return bool
  */
 function send_new_password_request($user_guid) {
-	global $CONFIG;
-
 	$user_guid = (int)$user_guid;
 
 	$user = get_entity($user_guid);
-	if ($user) {
+	if ($user instanceof ElggUser) {
 		// generate code
 		$code = generate_random_cleartext_password();
 		$user->setPrivateSetting('passwd_conf_code', $code);
 
-
 		// generate link
-		$link = $CONFIG->site->url . "resetpassword?u=$user_guid&c=$code";
+		$link = elgg_get_site_url() . "resetpassword?u=$user_guid&c=$code";
 
 		// generate email
 		$email = elgg_echo('email:resetreq:body', array($user->name, $_SERVER['REMOTE_ADDR'], $link));
 
-		return notify_user($user->guid, $CONFIG->site->guid,
-			elgg_echo('email:resetreq:subject'), $email, NULL, 'email');
+		return notify_user($user->guid, elgg_get_site_entity()->guid,
+			elgg_echo('email:resetreq:subject'), $email, array(), 'email');
 	}
 
 	return false;
@@ -713,8 +708,7 @@ function force_user_password_reset($user_guid, $password) {
 	global $CONFIG;
 
 	$user = get_entity($user_guid);
-
-	if ($user) {
+	if ($user instanceof ElggUser) {
 		$salt = generate_random_cleartext_password(); // Reset the salt
 		$user->salt = $salt;
 
@@ -742,7 +736,7 @@ function execute_new_password_request($user_guid, $conf_code) {
 	$user_guid = (int)$user_guid;
 	$user = get_entity($user_guid);
 
-	if ($user) {
+	if ($user instanceof ElggUser) {
 		$saved_code = $user->getPrivateSetting('passwd_conf_code');
 
 		if ($saved_code && $saved_code == $conf_code) {
@@ -756,7 +750,7 @@ function execute_new_password_request($user_guid, $conf_code) {
 				$email = elgg_echo('email:resetpassword:body', array($user->name, $password));
 
 				return notify_user($user->guid, $CONFIG->site->guid,
-					elgg_echo('email:resetpassword:subject'), $email, NULL, 'email');
+					elgg_echo('email:resetpassword:subject'), $email, array(), 'email');
 			}
 		}
 	}
@@ -841,7 +835,7 @@ function validate_username($username) {
 	for ($n = 0; $n < strlen($blacklist2); $n++) {
 		if (strpos($username, $blacklist2[$n]) !== false) {
 			$msg = elgg_echo('registration:invalidchars', array($blacklist2[$n], $blacklist2));
-			$msg = htmlentities($msg, ENT_COMPAT, 'UTF-8');
+			$msg = htmlspecialchars($msg, ENT_QUOTES, 'UTF-8');
 			throw new RegistrationException($msg);
 		}
 	}
@@ -908,13 +902,11 @@ function validate_email_address($address) {
  * @param string $invitecode            An invite code from a friend
  *
  * @return int|false The new user's GUID; false on failure
+ * @throws RegistrationException
  */
 function register_user($username, $password, $name, $email,
 $allow_multiple_emails = false, $friend_guid = 0, $invitecode = '') {
 
-	// Load the configuration
-	global $CONFIG;
-
 	// no need to trim password.
 	$username = trim($username);
 	$name = trim(strip_tags($name));
@@ -1031,7 +1023,7 @@ function elgg_get_user_validation_status($user_guid) {
 		'metadata_name' => 'validated'
 	));
 	if ($md == false) {
-		return;
+		return null;
 	}
 
 	if ($md[0]->value) {
@@ -1067,10 +1059,10 @@ function collections_submenu_items() {
  * @return bool
  * @access private
  */
-function friends_page_handler($page_elements, $handler) {
+function friends_page_handler($segments, $handler) {
 	elgg_set_context('friends');
 	
-	if (isset($page_elements[0]) && $user = get_user_by_username($page_elements[0])) {
+	if (isset($segments[0]) && $user = get_user_by_username($segments[0])) {
 		elgg_set_page_owner_guid($user->getGUID());
 	}
 	if (elgg_get_logged_in_user_guid() == elgg_get_page_owner_guid()) {
@@ -1197,13 +1189,11 @@ function set_last_login($user_guid) {
  * @param string   $object_type user
  * @param ElggUser $object      User object
  *
- * @return bool
+ * @return void
  * @access private
  */
 function user_create_hook_add_site_relationship($event, $object_type, $object) {
-	global $CONFIG;
-
-	add_entity_relationship($object->getGUID(), 'member_of_site', $CONFIG->site->getGUID());
+	add_entity_relationship($object->getGUID(), 'member_of_site', elgg_get_site_entity()->guid);
 }
 
 /**
@@ -1233,6 +1223,7 @@ function user_avatar_hook($hook, $entity_type, $returnvalue, $params) {
  */
 function elgg_user_hover_menu($hook, $type, $return, $params) {
 	$user = $params['entity'];
+	/* @var ElggUser $user */
 
 	if (elgg_is_logged_in()) {
 		if (elgg_get_logged_in_user_guid() != $user->guid) {
@@ -1309,7 +1300,12 @@ function elgg_user_hover_menu($hook, $type, $return, $params) {
 /**
  * Setup the menu shown with an entity
  *
+ * @param string $hook
+ * @param string $type
+ * @param array $return
+ * @param array $params
  * @return array
+ *
  * @access private
  */
 function elgg_users_setup_entity_menu($hook, $type, $return, $params) {
@@ -1321,6 +1317,7 @@ function elgg_users_setup_entity_menu($hook, $type, $return, $params) {
 	if (!elgg_instanceof($entity, 'user')) {
 		return $return;
 	}
+	/* @var ElggUser $entity */
 
 	if ($entity->isBanned()) {
 		$banned = elgg_echo('banned');
@@ -1334,9 +1331,10 @@ function elgg_users_setup_entity_menu($hook, $type, $return, $params) {
 	} else {
 		$return = array();
 		if (isset($entity->location)) {
+			$location = htmlspecialchars($entity->location, ENT_QUOTES, 'UTF-8', false);
 			$options = array(
 				'name' => 'location',
-				'text' => "<span>$entity->location</span>",
+				'text' => "<span>$location</span>",
 				'href' => false,
 				'priority' => 150,
 			);
@@ -1587,7 +1585,7 @@ function users_init() {
 /**
  * Runs unit tests for ElggObject
  *
- * @param sting  $hook   unit_test
+ * @param string $hook   unit_test
  * @param string $type   system
  * @param mixed  $value  Array of tests
  * @param mixed  $params Params
diff --git a/engine/lib/views.php b/engine/lib/views.php
index 01291b889..cfceccec0 100644
--- a/engine/lib/views.php
+++ b/engine/lib/views.php
@@ -1308,7 +1308,7 @@ function elgg_view_form($action, $form_vars = array(), $body_vars = array()) {
 /**
  * View an item in a list
  *
- * @param object $item ElggEntity or ElggAnnotation
+ * @param ElggEntity|ElggAnnotation $item
  * @param array  $vars Additional parameters for the rendering
  *
  * @return string
@@ -1451,17 +1451,13 @@ function elgg_get_views($dir, $base) {
  */
 function elgg_view_tree($view_root, $viewtype = "") {
 	global $CONFIG;
-	static $treecache;
+	static $treecache = array();
 
 	// Get viewtype
 	if (!$viewtype) {
 		$viewtype = elgg_get_viewtype();
 	}
 
-	// Has the treecache been initialised?
-	if (!isset($treecache)) {
-		$treecache = array();
-	}
 	// A little light internal caching
 	if (!empty($treecache[$view_root])) {
 		return $treecache[$view_root];
diff --git a/engine/lib/web_services.php b/engine/lib/web_services.php
index c8e4a13cc..b440e3afb 100644
--- a/engine/lib/web_services.php
+++ b/engine/lib/web_services.php
@@ -178,7 +178,7 @@ function authenticate_method($method) {
 	// check if user authentication is required
 	if ($API_METHODS[$method]["require_user_auth"] == true) {
 		if ($user_auth_result == false) {
-			throw new APIException($user_pam->getFailureMessage());
+			throw new APIException($user_pam->getFailureMessage(), ErrorResult::$RESULT_FAIL_AUTHTOKEN);
 		}
 	}
 
@@ -1267,14 +1267,14 @@ function service_handler($handler, $request) {
 	$request = explode('/', $request);
 
 	// after the handler, the first identifier is response format
-	// ex) http://example.org/services/api/rest/xml/?method=test
-	$reponse_format = array_shift($request);
+	// ex) http://example.org/services/api/rest/json/?method=test
+	$response_format = array_shift($request);
 	// Which view - xml, json, ...
-	if ($reponse_format) {
-		elgg_set_viewtype($reponse_format);
+	if ($response_format && elgg_is_valid_view_type($response_format)) {
+		elgg_set_viewtype($response_format);
 	} else {
-		// default to xml
-		elgg_set_viewtype("xml");
+		// default to json
+		elgg_set_viewtype("json");
 	}
 
 	if (!isset($CONFIG->servicehandler) || empty($handler)) {
diff --git a/engine/lib/widgets.php b/engine/lib/widgets.php
index d73dd6330..699462a1b 100644
--- a/engine/lib/widgets.php
+++ b/engine/lib/widgets.php
@@ -336,7 +336,7 @@ function elgg_default_widgets_init() {
  *
  * @param string $event  The event
  * @param string $type   The type of object
- * @param object $entity The entity being created
+ * @param ElggEntity $entity The entity being created
  * @return void
  * @access private
  */
@@ -372,6 +372,7 @@ function elgg_create_default_widgets($event, $type, $entity) {
 				);
 
 				$widgets = elgg_get_entities_from_private_settings($options);
+				/* @var ElggWidget[] $widgets */
 
 				foreach ($widgets as $widget) {
 					// change the container and owner
diff --git a/engine/lib/xml.php b/engine/lib/xml.php
index ff82d7e8a..497459d83 100644
--- a/engine/lib/xml.php
+++ b/engine/lib/xml.php
@@ -104,7 +104,7 @@ function serialise_array_to_xml(array $data, $n = 0) {
  *
  * @param string $xml The XML
  *
- * @return object
+ * @return ElggXMLElement
  */
 function xml_to_object($xml) {
 	return new ElggXMLElement($xml);
diff --git a/engine/tests/api/entity_getter_functions.php b/engine/tests/api/entity_getter_functions.php
index 9db248de9..7bf8ef04a 100644
--- a/engine/tests/api/entity_getter_functions.php
+++ b/engine/tests/api/entity_getter_functions.php
@@ -426,7 +426,7 @@ class ElggCoreEntityGetterFunctionsTest extends ElggCoreUnitTest {
 
 		$options = array(
 			'types' => $types,
-			'subtypes' => $subtype
+			'subtype' => $subtype
 		);
 
 		$es = elgg_get_entities($options);
@@ -2648,7 +2648,7 @@ class ElggCoreEntityGetterFunctionsTest extends ElggCoreUnitTest {
 			$name = 'test_annotation_' . rand(0, 9999);
 			$values = array();
 			$options = array(
-				'types' => 'object',
+				'type' => 'object',
 				'subtypes' => $subtypes,
 				'limit' => 5
 			);
@@ -2687,7 +2687,7 @@ class ElggCoreEntityGetterFunctionsTest extends ElggCoreUnitTest {
 			$order = array_keys($values);
 
 			$options = array(
-				'types' => 'object',
+				'type' => 'object',
 				'subtypes' => $subtypes,
 				'limit' => 5,
 				'annotation_name' => $name,
@@ -2729,6 +2729,36 @@ class ElggCoreEntityGetterFunctionsTest extends ElggCoreUnitTest {
 		}
 	}
 
+	public function testElggGetEntitiesFromAnnotationCalculationCount() {
+		// add two annotations with a unique name to an entity
+		// then count the number of entities with that annotation name
+
+		$subtypes = $this->getRandomValidSubtypes(array('object'), 1);
+		$name = 'test_annotation_' . rand(0, 9999);
+		$values = array();
+		$options = array(
+			'type' => 'object',
+			'subtypes' => $subtypes,
+			'limit' => 1
+		);
+		$es = elgg_get_entities($options);
+		$entity = $es[0];
+		$value = rand(0, 9999);
+		$entity->annotate($name, $value);
+		$value = rand(0, 9999);
+		$entity->annotate($name, $value);
+
+		$options = array(
+			'type' => 'object',
+			'subtypes' => $subtypes,
+			'annotation_name' => $name,
+			'calculation' => 'count',
+			'count' => true,
+		);
+		$count = (int)elgg_get_entities_from_annotation_calculation($options);
+		$this->assertEqual(1, $count);
+	}
+
 	public function testElggGetAnnotationsAnnotationNames() {
 		$options = array('annotation_names' => array());
 		$a_e_map = array();
@@ -2817,4 +2847,38 @@ class ElggCoreEntityGetterFunctionsTest extends ElggCoreUnitTest {
 		$entities = elgg_get_entities($options);
 		$this->assertFalse($entities);
 	}
+
+	public function testEGEEmptySubtypePlurality() {
+		$options = array(
+			'type' => 'user',
+			'subtypes' => ''
+		);
+
+		$entities = elgg_get_entities($options);
+		$this->assertTrue(is_array($entities));
+
+		$options = array(
+			'type' => 'user',
+			'subtype' => ''
+		);
+
+		$entities = elgg_get_entities($options);
+		$this->assertTrue(is_array($entities));
+
+		$options = array(
+			'type' => 'user',
+			'subtype' => array('')
+		);
+
+		$entities = elgg_get_entities($options);
+		$this->assertTrue(is_array($entities));
+
+		$options = array(
+			'type' => 'user',
+			'subtypes' => array('')
+		);
+
+		$entities = elgg_get_entities($options);
+		$this->assertTrue(is_array($entities));
+	}
 }