Merge branch 'release/1.8.1'

106 files changed, 2532 insertions, 860 deletions

diff --git a/engine/classes/ElggAccess.php b/engine/classes/ElggAccess.php
index 6f8d9bb4b..0aed477fc 100644
--- a/engine/classes/ElggAccess.php
+++ b/engine/classes/ElggAccess.php
@@ -16,6 +16,7 @@ class ElggAccess {
 	 */
 	private $ignore_access;
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Get current ignore access setting.
 	 *
@@ -26,6 +27,7 @@ class ElggAccess {
 		elgg_deprecated_notice('ElggAccess::get_ignore_access() is deprecated by ElggAccess::getIgnoreAccess()', 1.8);
 		return $this->getIgnoreAccess();
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Get current ignore access setting.
@@ -36,6 +38,7 @@ class ElggAccess {
 		return $this->ignore_access;
 	}
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Set ignore access.
 	 *
@@ -49,6 +52,7 @@ class ElggAccess {
 		elgg_deprecated_notice('ElggAccess::set_ignore_access() is deprecated by ElggAccess::setIgnoreAccess()', 1.8);
 		return $this->setIgnoreAccess($ignore);
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Set ignore access.
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..ffc80b02d 100644
--- a/engine/classes/ElggAttributeLoader.php
+++ b/engine/classes/ElggAttributeLoader.php
@@ -4,6 +4,9 @@
  * Loads ElggEntity attributes from DB or validates those passed in via constructor
  *
  * @access private
+ *
+ * @package    Elgg.Core
+ * @subpackage DataModel
  */
 class ElggAttributeLoader {
 
@@ -21,7 +24,7 @@ class ElggAttributeLoader {
 		'time_created',
 		'time_updated',
 		'last_action',
-		'enabled'
+		'enabled',
 	);
 
 	/**
@@ -65,9 +68,11 @@ class ElggAttributeLoader {
 	public $full_loader = '';
 
 	/**
-	 * @param string $class class of object being loaded
-	 * @param string $required_type entity type this is being used to populate
-	 * @param array $initialized_attrs attributes after initializeAttributes() has been run
+	 * Constructor
+	 *
+	 * @param string $class             class of object being loaded
+	 * @param string $required_type     entity type this is being used to populate
+	 * @param array  $initialized_attrs attributes after initializeAttributes() has been run
 	 * @throws InvalidArgumentException
 	 */
 	public function __construct($class, $required_type, array $initialized_attrs) {
@@ -87,14 +92,33 @@ class ElggAttributeLoader {
 		$this->secondary_attr_names = array_diff($all_attr_names, self::$primary_attr_names);
 	}
 
+	/**
+	 * Get primary attributes missing that are missing
+	 *
+	 * @param stdClass $row Database row
+	 * @return array
+	 */
 	protected function isMissingPrimaries($row) {
 		return array_diff(self::$primary_attr_names, array_keys($row)) !== array();
 	}
 
+	/**
+	 * Get secondary attributes that are missing
+	 *
+	 * @param stdClass $row Database row
+	 * @return array
+	 */
 	protected function isMissingSecondaries($row) {
 		return array_diff($this->secondary_attr_names, array_keys($row)) !== array();
 	}
 
+	/**
+	 * Check that the type is correct
+	 *
+	 * @param stdClass $row Database row
+	 * @return void
+	 * @throws InvalidClassException
+	 */
 	protected function checkType($row) {
 		if ($row['type'] !== $this->required_type) {
 			$msg = elgg_echo('InvalidClassException:NotValidElggStar', array($row['guid'], $this->class));
@@ -148,11 +172,11 @@ class ElggAttributeLoader {
 				if (!is_callable($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) {
@@ -176,6 +200,8 @@ class ElggAttributeLoader {
 						// saved, these are stored w/ type "site", but with no sites_entity row. These
 						// are probably only created in the unit tests.
 						// @todo Don't save vanilla ElggEntities with type "site"
+
+						$row = $this->filterAddedColumns($row);
 						$row['guid'] = (int) $row['guid'];
 						return $row;
 					}
@@ -185,15 +211,38 @@ class ElggAttributeLoader {
 			}
 		}
 
-		// loading complete: re-check missing and check type
-		if (($was_missing_primaries && $this->isMissingPrimaries($row))
-				|| ($was_missing_secondaries && $this->isMissingSecondaries($row))) {
-			throw new LogicException('Attribute loaders failed to return proper attributes');
-		}
+		$row = $this->filterAddedColumns($row);
+
+		// Note: If there are still missing attributes, we're running on a 1.7 or earlier schema. We let
+		// this pass so the upgrades can run.
 
-		// guid needs to be an int  http://trac.elgg.org/ticket/4111
+		// guid needs to be an int  https://github.com/elgg/elgg/issues/4111
 		$row['guid'] = (int) $row['guid'];
 
 		return $row;
 	}
+
+	/**
+	 * Filter out keys returned by the query which should not appear in the entity's attributes
+	 *
+	 * @param array $row All columns from the query
+	 * @return array Columns acceptable for the entity's attributes
+	 */
+	protected function filterAddedColumns($row) {
+		// make an array with keys as acceptable attribute names
+		$acceptable_attrs = self::$primary_attr_names;
+		array_splice($acceptable_attrs, count($acceptable_attrs), 0, $this->secondary_attr_names);
+		$acceptable_attrs = array_combine($acceptable_attrs, $acceptable_attrs);
+
+		// @todo remove these when #4584 is in place
+		$acceptable_attrs['tables_split'] = true;
+		$acceptable_attrs['tables_loaded'] = true;
+
+		foreach ($row as $key => $val) {
+			if (!isset($acceptable_attrs[$key])) {
+				unset($row[$key]);
+			}
+		}
+		return $row;
+	}
 }
diff --git a/engine/classes/ElggAutoP.php b/engine/classes/ElggAutoP.php
index 89d77e583..05842d1b2 100644
--- a/engine/classes/ElggAutoP.php
+++ b/engine/classes/ElggAutoP.php
@@ -7,6 +7,9 @@
  *
  * In DIV elements, Ps are only added when there would be at
  * least two of them.
+ * 
+ * @package    Elgg.Core
+ * @subpackage Output
  */
 class ElggAutoP {
 
@@ -51,8 +54,12 @@ class ElggAutoP {
 	protected $_alterList = 'article aside blockquote body details div footer header
 		section';
 
+	/** @var string */
 	protected $_unique = '';
 
+	/**
+	 * Constructor
+	 */
 	public function __construct() {
 		$this->_blocks = preg_split('@\\s+@', $this->_blocks);
 		$this->_descendList = preg_split('@\\s+@', $this->_descendList);
@@ -98,25 +105,34 @@ class ElggAutoP {
 		$html = str_replace('&', $this->_unique . 'AMP', $html);
 
 		$this->_doc = new DOMDocument();
-	   
+
 		// parse to DOM, suppressing loadHTML warnings
 		// http://www.php.net/manual/en/domdocument.loadhtml.php#95463
 		libxml_use_internal_errors(true);
 
+		// Do not load entities. May be unnecessary, better safe than sorry
+		$disable_load_entities = libxml_disable_entity_loader(true);
+
 		if (!$this->_doc->loadHTML("<html><meta http-equiv='content-type' " 
 				. "content='text/html; charset={$this->encoding}'><body>{$html}</body>"
 				. "</html>")) {
+
+			libxml_disable_entity_loader($disable_load_entities);
 			return false;
 		}
 
+		libxml_disable_entity_loader($disable_load_entities);
+
 		$this->_xpath = new DOMXPath($this->_doc);
 		// start processing recursively at the BODY element
 		$nodeList = $this->_xpath->query('//body[1]');
-		$this->_addParagraphs($nodeList->item(0));
+		$this->addParagraphs($nodeList->item(0));
 
 		// 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>'), 
@@ -126,14 +142,22 @@ class ElggAutoP {
 
 		// re-parse so we can handle new AUTOP elements
 
+		// Do not load entities. May be unnecessary, better safe than sorry
+		$disable_load_entities = libxml_disable_entity_loader(true);
+
 		if (!$this->_doc->loadHTML($html)) {
+			libxml_disable_entity_loader($disable_load_entities);
 			return false;
 		}
+
+		libxml_disable_entity_loader($disable_load_entities);
+
 		// must re-create XPath object after DOM load
 		$this->_xpath = new DOMXPath($this->_doc);
 
 		// strip AUTOPs that only have comments/whitespace
 		foreach ($this->_xpath->query('//autop') as $autop) {
+			/* @var DOMElement $autop */
 			$hasContent = false;
 			if (trim($autop->textContent) !== '') {
 				$hasContent = true;
@@ -146,17 +170,19 @@ class ElggAutoP {
 				}
 			}
 			if (!$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");
 			}
 		}
 
@@ -182,15 +208,16 @@ class ElggAutoP {
 	/**
 	 * Add P and BR elements as necessary
 	 *
-	 * @param DOMElement $el
+	 * @param DOMElement $el DOM element
+	 * @return void
 	 */
-	protected function _addParagraphs(DOMElement $el) {
-		// no need to recurse, just queue up
+	protected function addParagraphs(DOMElement $el) {
+		// no need to call recursively, just queue up
 		$elsToProcess = array($el);
 		$inlinesToProcess = array();
 		while ($el = array_shift($elsToProcess)) {
 			// if true, we can alter all child nodes, if not, we'll just call
-			// _addParagraphs on each element in the descendInto list
+			// addParagraphs on each element in the descendInto list
 			$alterInline = in_array($el->nodeName, $this->_alterList);
 
 			// inside affected elements, we want to trim leading whitespace from
@@ -216,16 +243,16 @@ 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
-									   && in_array($node->nextSibling->nodeName, $this->_blocks)));
+							|| ($node->nextSibling->nodeType === XML_ELEMENT_NODE
+								&& in_array($node->nextSibling->nodeName, $this->_blocks)));
 					if ($isElement) {
 						$isFollowingBr = ($node->nodeName === 'br');
 					}
@@ -258,7 +285,7 @@ class ElggAutoP {
 					if ($isBlock) {
 						if (in_array($node->nodeName, $this->_descendList)) {
 							$elsToProcess[] = $node;
-							//$this->_addParagraphs($node);
+							//$this->addParagraphs($node);
 						}
 					}
 					$openP = true;
diff --git a/engine/classes/ElggBatch.php b/engine/classes/ElggBatch.php
index c1a77a0d9..d810ea066 100644
--- a/engine/classes/ElggBatch.php
+++ b/engine/classes/ElggBatch.php
@@ -150,6 +150,20 @@ class ElggBatch
 	private $incrementOffset = true;
 
 	/**
+	 * Entities that could not be instantiated during a fetch
+	 *
+	 * @var stdClass[]
+	 */
+	private $incompleteEntities = array();
+
+	/**
+	 * Total number of incomplete entities fetched
+	 *
+	 * @var int
+	 */
+	private $totalIncompletes = 0;
+
+	/**
 	 * Batches operations on any elgg_get_*() or compatible function that supports
 	 * an options array.
 	 *
@@ -222,16 +236,22 @@ class ElggBatch
 	}
 
 	/**
+	 * Tell the process that an entity was incomplete during a fetch
+	 *
+	 * @param stdClass $row
+	 *
+	 * @access private
+	 */
+	public function reportIncompleteEntity(stdClass $row) {
+		$this->incompleteEntities[] = $row;
+	}
+
+	/**
 	 * Fetches the next chunk of results
 	 *
 	 * @return bool
 	 */
 	private function getNextResultsChunk() {
-		// reset memory caches after first chunk load
-		if ($this->chunkIndex > 0) {
-			global $DB_QUERY_CACHE, $ENTITY_CACHE;
-			$DB_QUERY_CACHE = $ENTITY_CACHE = array();
-		}
 
 		// always reset results.
 		$this->results = array();
@@ -265,27 +285,47 @@ class ElggBatch
 		if ($this->incrementOffset) {
 			$offset = $this->offset + $this->retrievedResults;
 		} else {
-			$offset = $this->offset;
+			$offset = $this->offset + $this->totalIncompletes;
 		}
 
 		$current_options = array(
 			'limit' => $limit,
-			'offset' => $offset
+			'offset' => $offset,
+			'__ElggBatch' => $this,
 		);
 
 		$options = array_merge($this->options, $current_options);
-		$getter = $this->getter;
 
-		if (is_string($getter)) {
-			$this->results = $getter($options);
-		} else {
-			$this->results = call_user_func_array($getter, array($options));
+		$this->incompleteEntities = array();
+		$this->results = call_user_func_array($this->getter, array($options));
+
+		$num_results = count($this->results);
+		$num_incomplete = count($this->incompleteEntities);
+
+		$this->totalIncompletes += $num_incomplete;
+
+		if ($this->incompleteEntities) {
+			// pad the front of the results with nulls representing the incompletes
+			array_splice($this->results, 0, 0, array_pad(array(), $num_incomplete, null));
+			// ...and skip past them
+			reset($this->results);
+			for ($i = 0; $i < $num_incomplete; $i++) {
+				next($this->results);
+			}
 		}
 
 		if ($this->results) {
 			$this->chunkIndex++;
-			$this->resultIndex = 0;
-			$this->retrievedResults += count($this->results);
+
+			// let the system know we've jumped past the nulls
+			$this->resultIndex = $num_incomplete;
+
+			$this->retrievedResults += ($num_results + $num_incomplete);
+			if ($num_results == 0) {
+				// This fetch was *all* incompletes! We need to fetch until we can either
+				// offer at least one row to iterate over, or give up.
+				return $this->getNextResultsChunk();
+			}
 			return true;
 		} else {
 			return false;
@@ -296,7 +336,8 @@ 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/ElggCache.php b/engine/classes/ElggCache.php
index 4317f4be9..909eab39b 100644
--- a/engine/classes/ElggCache.php
+++ b/engine/classes/ElggCache.php
@@ -21,6 +21,7 @@ abstract class ElggCache implements ArrayAccess {
 		$this->variables = array();
 	}
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Set a cache variable.
 	 *
@@ -35,6 +36,7 @@ abstract class ElggCache implements ArrayAccess {
 		elgg_deprecated_notice('ElggCache::set_variable() is deprecated by ElggCache::setVariable()', 1.8);
 		$this->setVariable($variable, $value);
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Set a cache variable.
@@ -52,6 +54,7 @@ abstract class ElggCache implements ArrayAccess {
 		$this->variables[$variable] = $value;
 	}
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Get variables for this cache.
 	 *
@@ -65,6 +68,7 @@ abstract class ElggCache implements ArrayAccess {
 		elgg_deprecated_notice('ElggCache::get_variable() is deprecated by ElggCache::getVariable()', 1.8);
 		return $this->getVariable($variable);
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Get variables for this cache.
diff --git a/engine/classes/ElggCrypto.php b/engine/classes/ElggCrypto.php
new file mode 100644
index 000000000..317d371e4
--- /dev/null
+++ b/engine/classes/ElggCrypto.php
@@ -0,0 +1,208 @@
+<?php
+/**
+ * ElggCrypto
+ *
+ * @package    Elgg.Core
+ * @subpackage Crypto
+ *
+ * @access private
+ */
+class ElggCrypto {
+
+	/**
+	 * Character set for temp passwords (no risk of embedded profanity/glyphs that look similar)
+	 */
+	const CHARS_PASSWORD = 'bcdfghjklmnpqrstvwxyz2346789';
+
+	/**
+	 * Generate a string of highly randomized bytes (over the full 8-bit range).
+	 *
+	 * @param int $length Number of bytes needed
+	 * @return string Random bytes
+	 *
+	 * @author George Argyros <argyros.george@gmail.com>
+	 * @copyright 2012, George Argyros. All rights reserved.
+	 * @license Modified BSD
+	 * @link https://github.com/GeorgeArgyros/Secure-random-bytes-in-PHP/blob/master/srand.php Original
+	 *
+	 * Redistribution and use in source and binary forms, with or without
+	 * modification, are permitted provided that the following conditions are met:
+	 *    * Redistributions of source code must retain the above copyright
+	 *      notice, this list of conditions and the following disclaimer.
+	 *    * Redistributions in binary form must reproduce the above copyright
+	 *      notice, this list of conditions and the following disclaimer in the
+	 *      documentation and/or other materials provided with the distribution.
+	 *    * Neither the name of the <organization> nor the
+	 *      names of its contributors may be used to endorse or promote products
+	 *      derived from this software without specific prior written permission.
+	 *
+	 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+	 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+	 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+	 * DISCLAIMED. IN NO EVENT SHALL GEORGE ARGYROS BE LIABLE FOR ANY
+	 * DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+	 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+	 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+	 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+	 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+	 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+	 */
+	public function getRandomBytes($length) {
+		/**
+		 * Our primary choice for a cryptographic strong randomness function is
+		 * openssl_random_pseudo_bytes.
+		 */
+		$SSLstr = '4'; // http://xkcd.com/221/
+		if (function_exists('openssl_random_pseudo_bytes')
+				&& (version_compare(PHP_VERSION, '5.3.4') >= 0 || substr(PHP_OS, 0, 3) !== 'WIN')) {
+			$SSLstr = openssl_random_pseudo_bytes($length, $strong);
+			if ($strong) {
+				return $SSLstr;
+			}
+		}
+
+		/**
+		 * If mcrypt extension is available then we use it to gather entropy from
+		 * the operating system's PRNG. This is better than reading /dev/urandom
+		 * directly since it avoids reading larger blocks of data than needed.
+		 * Older versions of mcrypt_create_iv may be broken or take too much time
+		 * to finish so we only use this function with PHP 5.3.7 and above.
+		 * @see https://bugs.php.net/bug.php?id=55169
+		 */
+		if (function_exists('mcrypt_create_iv')
+				&& (version_compare(PHP_VERSION, '5.3.7') >= 0 || substr(PHP_OS, 0, 3) !== 'WIN')) {
+			$str = mcrypt_create_iv($length, MCRYPT_DEV_URANDOM);
+			if ($str !== false) {
+				return $str;
+			}
+		}
+
+		/**
+		 * No build-in crypto randomness function found. We collect any entropy
+		 * available in the PHP core PRNGs along with some filesystem info and memory
+		 * stats. To make this data cryptographically strong we add data either from
+		 * /dev/urandom or if its unavailable, we gather entropy by measuring the
+		 * time needed to compute a number of SHA-1 hashes.
+		 */
+		$str = '';
+		$bits_per_round = 2; // bits of entropy collected in each clock drift round
+		$msec_per_round = 400; // expected running time of each round in microseconds
+		$hash_len = 20; // SHA-1 Hash length
+		$total = $length; // total bytes of entropy to collect
+
+		$handle = @fopen('/dev/urandom', 'rb');
+		if ($handle && function_exists('stream_set_read_buffer')) {
+			@stream_set_read_buffer($handle, 0);
+		}
+
+		do {
+			$bytes = ($total > $hash_len) ? $hash_len : $total;
+			$total -= $bytes;
+
+			//collect any entropy available from the PHP system and filesystem
+			$entropy = rand() . uniqid(mt_rand(), true) . $SSLstr;
+			$entropy .= implode('', @fstat(@fopen(__FILE__, 'r')));
+			$entropy .= memory_get_usage() . getmypid();
+			$entropy .= serialize($_ENV) . serialize($_SERVER);
+			if (function_exists('posix_times')) {
+				$entropy .= serialize(posix_times());
+			}
+			if (function_exists('zend_thread_id')) {
+				$entropy .= zend_thread_id();
+			}
+
+			if ($handle) {
+				$entropy .= @fread($handle, $bytes);
+			} else {
+				// Measure the time that the operations will take on average
+				for ($i = 0; $i < 3; $i++) {
+					$c1 = microtime(true);
+					$var = sha1(mt_rand());
+					for ($j = 0; $j < 50; $j++) {
+						$var = sha1($var);
+					}
+					$c2 = microtime(true);
+					$entropy .= $c1 . $c2;
+				}
+
+				// Based on the above measurement determine the total rounds
+				// in order to bound the total running time.
+				$rounds = (int) ($msec_per_round * 50 / (int) (($c2 - $c1) * 1000000));
+
+				// Take the additional measurements. On average we can expect
+				// at least $bits_per_round bits of entropy from each measurement.
+				$iter = $bytes * (int) (ceil(8 / $bits_per_round));
+
+				for ($i = 0; $i < $iter; $i++) {
+					$c1 = microtime();
+					$var = sha1(mt_rand());
+					for ($j = 0; $j < $rounds; $j++) {
+						$var = sha1($var);
+					}
+					$c2 = microtime();
+					$entropy .= $c1 . $c2;
+				}
+			}
+
+			// We assume sha1 is a deterministic extractor for the $entropy variable.
+			$str .= sha1($entropy, true);
+
+		} while ($length > strlen($str));
+
+		if ($handle) {
+			@fclose($handle);
+		}
+
+		return substr($str, 0, $length);
+	}
+
+	/**
+	 * Generate a random string of specified length.
+	 *
+	 * Uses supplied character list for generating the new string.
+	 * If no character list provided - uses Base64 URL character set.
+	 *
+	 * @param int         $length Desired length of the string
+	 * @param string|null $chars  Characters to be chosen from randomly. If not given, the Base64 URL
+	 *                            charset will be used.
+	 *
+	 * @return string The random string
+	 *
+	 * @throws InvalidArgumentException
+	 *
+	 * @copyright Copyright (c) 2005-2013 Zend Technologies USA Inc. (http://www.zend.com)
+	 * @license   http://framework.zend.com/license/new-bsd New BSD License
+	 *
+	 * @see https://github.com/zendframework/zf2/blob/master/library/Zend/Math/Rand.php#L179
+	 */
+	public static function getRandomString($length, $chars = null) {
+		if ($length < 1) {
+			throw new InvalidArgumentException('Length should be >= 1');
+		}
+
+		if (empty($chars)) {
+			$numBytes = ceil($length * 0.75);
+			$bytes    = self::getRandomBytes($numBytes);
+			$string = substr(rtrim(base64_encode($bytes), '='), 0, $length);
+
+			// Base64 URL
+			return strtr($string, '+/', '-_');
+		}
+
+		$listLen = strlen($chars);
+
+		if ($listLen == 1) {
+			return str_repeat($chars, $length);
+		}
+
+		$bytes  = self::getRandomBytes($length);
+		$pos    = 0;
+		$result = '';
+		for ($i = 0; $i < $length; $i++) {
+			$pos     = ($pos + ord($bytes[$i])) % $listLen;
+			$result .= $chars[$pos];
+		}
+
+		return $result;
+	}
+}
diff --git a/engine/classes/ElggData.php b/engine/classes/ElggData.php
index 3470ee1cf..4f843cde4 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
@@ -23,6 +26,7 @@ abstract class ElggData implements
 	 */
 	protected $attributes = array();
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Initialise the attributes array.
 	 *
@@ -33,16 +37,15 @@ 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;
 		}
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Initialize the attributes array.
@@ -111,7 +114,7 @@ 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 +198,7 @@ abstract class ElggData implements
 	 *
 	 * @see Iterator::current()
 	 *
-	 * @return void
+	 * @return mixed
 	 */
 	public function current() {
 		return current($this->attributes);
@@ -206,7 +209,7 @@ abstract class ElggData implements
 	 *
 	 * @see Iterator::key()
 	 *
-	 * @return void
+	 * @return string
 	 */
 	public function key() {
 		return key($this->attributes);
@@ -228,7 +231,7 @@ abstract class ElggData implements
 	 *
 	 * @see Iterator::valid()
 	 *
-	 * @return void
+	 * @return bool
 	 */
 	public function valid() {
 		return $this->valid;
@@ -266,12 +269,13 @@ 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..6e2354012 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.
 	 */
@@ -193,11 +194,14 @@ class ElggDiskFilestore extends ElggFilestore {
 	}
 
 	/**
-	 * Returns the filename as saved on disk for an ElggFile object
+	 * Get the filename as saved on disk for an ElggFile object
+	 *
+	 * Returns an empty string if no filename set
 	 *
 	 * @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 = $file->getOwnerGuid();
@@ -211,7 +215,12 @@ class ElggDiskFilestore extends ElggFilestore {
 			throw new InvalidParameterException($msg);
 		}
 
-		return $this->dir_root . $this->makefileMatrix($owner_guid) . $file->getFilename();
+		$filename = $file->getFilename();
+		if (!$filename) {
+			return '';
+		}
+
+		return $this->dir_root . $this->makeFileMatrix($owner_guid) . $filename;
 	}
 
 	/**
@@ -219,7 +228,7 @@ class ElggDiskFilestore extends ElggFilestore {
 	 *
 	 * @param ElggFile $file File object
 	 *
-	 * @return mixed
+	 * @return string
 	 */
 	public function grabFile(ElggFile $file) {
 		return file_get_contents($file->getFilenameOnFilestore());
@@ -233,6 +242,9 @@ class ElggDiskFilestore extends ElggFilestore {
 	 * @return bool
 	 */
 	public function exists(ElggFile $file) {
+		if (!$file->getFilename()) {
+			return false;
+		}
 		return file_exists($this->getFilenameOnFilestore($file));
 	}
 
@@ -246,12 +258,13 @@ class ElggDiskFilestore extends ElggFilestore {
 	 */
 	public function getSize($prefix = '', $container_guid) {
 		if ($container_guid) {
-			return get_dir_size($this->dir_root . $this->makefileMatrix($container_guid) . $prefix);
+			return get_dir_size($this->dir_root . $this->makeFileMatrix($container_guid) . $prefix);
 		} else {
 			return false;
 		}
 	}
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Create a directory $dirroot
 	 *
@@ -266,6 +279,7 @@ class ElggDiskFilestore extends ElggFilestore {
 
 		return $this->makeDirectoryRoot($dirroot);
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Create a directory $dirroot
@@ -285,6 +299,7 @@ class ElggDiskFilestore extends ElggFilestore {
 		return true;
 	}
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Multibyte string tokeniser.
 	 *
@@ -315,30 +330,31 @@ class ElggDiskFilestore extends ElggFilestore {
 		} else {
 			return str_split($string);
 		}
-
-		return false;
 	}
+	// @codingStandardsIgnoreEnd
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Construct a file path matrix for an entity.
 	 *
 	 * @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) {
 		elgg_deprecated_notice('ElggDiskFilestore::make_file_matrix() is deprecated by ::makeFileMatrix()', 1.8);
 
-		return $this->makefileMatrix($identifier);
+		return $this->makeFileMatrix($identifier);
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Construct a file path matrix for an entity.
 	 *
 	 * @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);
@@ -352,6 +368,7 @@ class ElggDiskFilestore extends ElggFilestore {
 		return "$time_created/$entity->guid/";
 	}
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Construct a filename matrix.
 	 *
@@ -363,13 +380,14 @@ 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);
 
 		return $this->makeFileMatrix($guid);
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Returns a list of attributes to save to the database when saving
diff --git a/engine/classes/ElggEntity.php b/engine/classes/ElggEntity.php
index 929abceb2..a563f6fad 100644
--- a/engine/classes/ElggEntity.php
+++ b/engine/classes/ElggEntity.php
@@ -24,7 +24,7 @@
  *
  * @package    Elgg.Core
  * @subpackage DataModel.Entities
- * 
+ *
  * @property string $type           object, user, group, or site (read-only after save)
  * @property string $subtype        Further clarifies the nature of the entity (read-only after save)
  * @property int    $guid           The unique identifier for this entity (read only)
@@ -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
@@ -351,8 +352,8 @@ abstract class ElggEntity extends ElggData implements
 					'limit' => 0
 				);
 				// @todo in 1.9 make this return false if can't add metadata
-				// http://trac.elgg.org/ticket/4520
-				// 
+				// https://github.com/elgg/elgg/issues/4520
+				//
 				// need to remove access restrictions right now to delete
 				// because this is the expected behavior
 				$ia = elgg_set_ignore_access(true);
@@ -374,12 +375,11 @@ abstract class ElggEntity extends ElggData implements
 			}
 
 			return $result;
-		}
-
-		// unsaved entity. store in temp array
-		// returning single entries instead of an array of 1 element is decided in
-		// getMetaData(), just like pulling from the db.
-		else {
+		} else {
+			// unsaved entity. store in temp array
+			// returning single entries instead of an array of 1 element is decided in
+			// getMetaData(), just like pulling from the db.
+			//
 			// if overwrite, delete first
 			if (!$multiple || !isset($this->temp_metadata[$name])) {
 				$this->temp_metadata[$name] = array();
@@ -940,7 +940,7 @@ 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);
@@ -964,7 +964,7 @@ abstract class ElggEntity extends ElggData implements
 	 *
 	 * @tip Can be overridden by registering for the permissions_check:comment,
 	 * <entity type> plugin hook.
-	 * 
+	 *
 	 * @param int $user_guid User guid (default is logged in user)
 	 *
 	 * @return bool
@@ -1270,15 +1270,23 @@ abstract class ElggEntity extends ElggData implements
 	public function save() {
 		$guid = $this->getGUID();
 		if ($guid > 0) {
-			cache_entity($this);
 
-			return update_entity(
+			// See #5600. This ensures the lower level can_edit_entity() check will use a
+			// fresh entity from the DB so it sees the persisted owner_guid
+			_elgg_disable_caching_for_entity($guid);
+
+			$ret = update_entity(
 				$guid,
 				$this->get('owner_guid'),
 				$this->get('access_id'),
 				$this->get('container_guid'),
 				$this->get('time_created')
 			);
+
+			_elgg_enable_caching_for_entity($guid);
+			_elgg_cache_entity($this);
+
+			return $ret;
 		} else {
 			// Create a new entity (nb: using attribute array directly
 			// 'cos set function does something special!)
@@ -1320,7 +1328,7 @@ abstract class ElggEntity extends ElggData implements
 			$this->attributes['subtype'] = get_subtype_id($this->attributes['type'],
 				$this->attributes['subtype']);
 
-			cache_entity($this);
+			_elgg_cache_entity($this);
 
 			return $this->attributes['guid'];
 		}
@@ -1357,12 +1365,12 @@ abstract class ElggEntity extends ElggData implements
 				$this->attributes['tables_loaded']++;
 			}
 
-			// guid needs to be an int  http://trac.elgg.org/ticket/4111
+			// guid needs to be an int  https://github.com/elgg/elgg/issues/4111
 			$this->attributes['guid'] = (int)$this->attributes['guid'];
 
 			// Cache object handle
 			if ($this->attributes['guid']) {
-				cache_entity($this);
+				_elgg_cache_entity($this);
 			}
 
 			return true;
@@ -1668,9 +1676,11 @@ 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 +1742,6 @@ 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..23080834b 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()) {
@@ -270,9 +275,14 @@ class ElggFile extends ElggObject {
 	 */
 	public function delete() {
 		$fs = $this->getFilestore();
-		if ($fs->delete($this)) {
-			return parent::delete();
+		
+		$result = $fs->delete($this);
+		
+		if ($this->getGUID() && $result) {
+			$result = parent::delete();
 		}
+		
+		return $result;
 	}
 
 	/**
@@ -285,6 +295,7 @@ class ElggFile extends ElggObject {
 	public function seek($position) {
 		$fs = $this->getFilestore();
 
+		// @todo add seek() to ElggFilestore
 		return $fs->seek($this->handle, $position);
 	}
 
@@ -347,6 +358,8 @@ 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 +372,6 @@ 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 +400,7 @@ 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..94143f777 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);
@@ -24,6 +26,7 @@ class ElggFileCache extends ElggCache {
 		}
 	}
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Create and return a handle to a file.
 	 *
@@ -39,6 +42,7 @@ class ElggFileCache extends ElggCache {
 
 		return $this->createFile($filename, $rw);
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Create and return a handle to a file.
@@ -70,6 +74,7 @@ class ElggFileCache extends ElggCache {
 		return fopen($path . $filename, $rw);
 	}
 
+	// @codingStandardsIgnoreStart
 	/**
 	 * Create a sanitised filename for the file.
 	 *
@@ -84,6 +89,7 @@ class ElggFileCache extends ElggCache {
 
 		return $filename;
 	}
+	// @codingStandardsIgnoreEnd
 
 	/**
 	 * Create a sanitised filename for the file.
diff --git a/engine/classes/ElggGroup.php b/engine/classes/ElggGroup.php
index ea257f368..7e69b7a84 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();
@@ -48,21 +48,18 @@ class ElggGroup extends ElggEntity
 					$msg = elgg_echo('IOException:FailedToLoadGUID', array(get_class(), $guid->guid));
 					throw new IOException($msg);
 				}
-
-			// Is $guid is an ElggGroup? Use a copy constructor
 			} else if ($guid instanceof ElggGroup) {
+				// $guid is an ElggGroup so this is a copy constructor
 				elgg_deprecated_notice('This type of usage of the ElggGroup constructor was deprecated. Please use the clone method.', 1.7);
 
 				foreach ($guid->attributes as $key => $value) {
 					$this->attributes[$key] = $value;
 				}
-
-			// Is this is an ElggEntity but not an ElggGroup = ERROR!
 			} else if ($guid instanceof ElggEntity) {
+				// @todo why separate from else
 				throw new InvalidParameterException(elgg_echo('InvalidParameterException:NonElggGroup'));
-
-			// Is it a GUID
 			} else if (is_numeric($guid)) {
+				// $guid is a GUID so load entity
 				if (!$this->load($guid)) {
 					throw new IOException(elgg_echo('IOException:FailedToLoadGUID', array(get_class(), $guid)));
 				}
@@ -220,6 +217,7 @@ class ElggGroup extends ElggEntity
 	 * @return array|false
 	 */
 	public function getObjects($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 +231,7 @@ 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 +243,7 @@ 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 +284,7 @@ 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();
 		}
@@ -335,7 +335,7 @@ class ElggGroup extends ElggEntity
 
 		$this->attributes = $attrs;
 		$this->attributes['tables_loaded'] = 2;
-		cache_entity($this);
+		_elgg_cache_entity($this);
 
 		return true;
 	}
@@ -352,7 +352,12 @@ class ElggGroup extends ElggEntity
 		}
 
 		// Now save specific stuff
-		return create_group_entity($this->get('guid'), $this->get('name'), $this->get('description'));
+
+		_elgg_disable_caching_for_entity($this->guid);
+		$ret = create_group_entity($this->get('guid'), $this->get('name'), $this->get('description'));
+		_elgg_enable_caching_for_entity($this->guid);
+
+		return $ret;
 	}
 
 	// EXPORTABLE INTERFACE ////////////////////////////////////////////////////////////
diff --git a/engine/classes/ElggLRUCache.php b/engine/classes/ElggLRUCache.php
new file mode 100644
index 000000000..f51af2ed7
--- /dev/null
+++ b/engine/classes/ElggLRUCache.php
@@ -0,0 +1,181 @@
+<?php
+
+/**
+ * Least Recently Used Cache
+ *
+ * A fixed sized cache that removes the element used last when it reaches its
+ * size limit.
+ * 
+ * Based on https://github.com/cash/LRUCache
+ * 
+ * @access private
+ * 
+ * @package    Elgg.Core
+ * @subpackage Cache
+ */
+class ElggLRUCache implements ArrayAccess {
+	/** @var int */
+	protected $maximumSize;
+
+	/**
+	 * The front of the array contains the LRU element
+	 *
+	 * @var array
+	 */
+	protected $data = array();
+
+	/**
+	 * Create a LRU Cache
+	 *
+	 * @param int $size The size of the cache
+	 * @throws InvalidArgumentException
+	 */
+	public function __construct($size) {
+		if (!is_int($size) || $size <= 0) {
+			throw new InvalidArgumentException();
+		}
+		$this->maximumSize = $size;
+	}
+
+	/**
+	 * Get the value cached with this key
+	 *
+	 * @param int|string $key     The key. Strings that are ints are cast to ints.
+	 * @param mixed      $default The value to be returned if key not found. (Optional)
+	 * @return mixed
+	 */
+	public function get($key, $default = null) {
+		if (isset($this->data[$key])) {
+			$this->recordAccess($key);
+			return $this->data[$key];
+		} else {
+			return $default;
+		}
+	}
+
+	/**
+	 * Add something to the cache
+	 *
+	 * @param int|string $key   The key. Strings that are ints are cast to ints.
+	 * @param mixed      $value The value to cache
+	 * @return void
+	 */
+	public function set($key, $value) {
+		if (isset($this->data[$key])) {
+			$this->data[$key] = $value;
+			$this->recordAccess($key);
+		} else {
+			$this->data[$key] = $value;
+			if ($this->size() > $this->maximumSize) {
+				// remove least recently used element (front of array)
+				reset($this->data);
+				unset($this->data[key($this->data)]);
+			}
+		}
+	}
+
+	/**
+	 * Get the number of elements in the cache
+	 *
+	 * @return int
+	 */
+	public function size() {
+		return count($this->data);
+	}
+
+	/**
+	 * Does the cache contain an element with this key
+	 *
+	 * @param int|string $key The key
+	 * @return boolean
+	 */
+	public function containsKey($key) {
+		return isset($this->data[$key]);
+	}
+
+	/**
+	 * Remove the element with this key.
+	 *
+	 * @param int|string $key The key
+	 * @return mixed Value or null if not set
+	 */
+	public function remove($key) {
+		if (isset($this->data[$key])) {
+			$value = $this->data[$key];
+			unset($this->data[$key]);
+			return $value;
+		} else {
+			return null;
+		}
+	}
+
+	/**
+	 * Clear the cache
+	 * 
+	 * @return void
+	 */
+	public function clear() {
+		$this->data = array();
+	}
+
+	/**
+	 * Moves the element from current position to end of array
+	 * 
+	 * @param int|string $key The key
+	 * @return void
+	 */
+	protected function recordAccess($key) {
+		$value = $this->data[$key];
+		unset($this->data[$key]);
+		$this->data[$key] = $value;
+	}
+
+	/**
+	 * Assigns a value for the specified key
+	 *
+	 * @see ArrayAccess::offsetSet()
+	 *
+	 * @param int|string $key   The key to assign the value to.
+	 * @param mixed      $value The value to set.
+	 * @return void
+	 */
+	public function offsetSet($key, $value) {
+		$this->set($key, $value);
+	}
+
+	/**
+	 * Get the value for specified key
+	 *
+	 * @see ArrayAccess::offsetGet()
+	 *
+	 * @param int|string $key The key to retrieve.
+	 * @return mixed
+	 */
+	public function offsetGet($key) {
+		return $this->get($key);
+	}
+
+	/**
+	 * Unsets a key.
+	 *
+	 * @see ArrayAccess::offsetUnset()
+	 *
+	 * @param int|string $key The key to unset.
+	 * @return void
+	 */
+	public function offsetUnset($key) {
+		$this->remove($key);
+	}
+
+	/**
+	 * Does key exist?
+	 *
+	 * @see ArrayAccess::offsetExists()
+	 *
+	 * @param int|string $key A key to check for.
+	 * @return boolean
+	 */
+	public function offsetExists($key) {
+		return $this->containsKey($key);
+	}
+}
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..b463143d8 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;
@@ -118,13 +122,16 @@ 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 = $menu_item->getParentName();
 					if (array_key_exists($parent_name, $current_gen)) {
 						$next_gen[$menu_item->getName()] = $menu_item;
-						$current_gen[$parent_name]->addChild($menu_item);
-						$menu_item->setParent($current_gen[$parent_name]);
+						if (!in_array($menu_item, $current_gen[$parent_name]->getData('children'))) {
+							$current_gen[$parent_name]->addChild($menu_item);
+							$menu_item->setParent($current_gen[$parent_name]);
+						}
 						unset($children[$index]);
 					}
 				}
@@ -216,12 +223,12 @@ class ElggMenuBuilder {
 				array_push($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);
 				}
 			}
 		}
@@ -230,8 +237,8 @@ class ElggMenuBuilder {
 	/**
 	 * Compare two menu items by their display text
 	 *
-	 * @param ElggMenuItem $a
-	 * @param ElggMenuItem $b
+	 * @param ElggMenuItem $a Menu item
+	 * @param ElggMenuItem $b Menu item
 	 * @return bool
 	 */
 	public static function compareByText($a, $b) {
@@ -248,8 +255,8 @@ class ElggMenuBuilder {
 	/**
 	 * Compare two menu items by their identifiers
 	 *
-	 * @param ElggMenuItem $a
-	 * @param ElggMenuItem $b
+	 * @param ElggMenuItem $a Menu item
+	 * @param ElggMenuItem $b Menu item
 	 * @return bool
 	 */
 	public static function compareByName($a, $b) {
@@ -266,9 +273,11 @@ class ElggMenuBuilder {
 	/**
 	 * Compare two menu items by their priority
 	 *
-	 * @param ElggMenuItem $a
-	 * @param ElggMenuItem $b
+	 * @param ElggMenuItem $a Menu item
+	 * @param ElggMenuItem $b Menu item
 	 * @return bool
+	 *
+	 * @todo change name to compareByPriority
 	 */
 	public static function compareByWeight($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/ElggObject.php b/engine/classes/ElggObject.php
index 6263f84f6..aeaa3ba5c 100644
--- a/engine/classes/ElggObject.php
+++ b/engine/classes/ElggObject.php
@@ -66,21 +66,18 @@ class ElggObject extends ElggEntity {
 					$msg = elgg_echo('IOException:FailedToLoadGUID', array(get_class(), $guid->guid));
 					throw new IOException($msg);
 				}
-
-			// Is $guid is an ElggObject? Use a copy constructor
 			} else if ($guid instanceof ElggObject) {
+				// $guid is an ElggObject so this is a copy constructor
 				elgg_deprecated_notice('This type of usage of the ElggObject constructor was deprecated. Please use the clone method.', 1.7);
 
 				foreach ($guid->attributes as $key => $value) {
 					$this->attributes[$key] = $value;
 				}
-
-			// Is this is an ElggEntity but not an ElggObject = ERROR!
 			} else if ($guid instanceof ElggEntity) {
+				// @todo remove - do not need separate exception
 				throw new InvalidParameterException(elgg_echo('InvalidParameterException:NonElggObject'));
-
-			// Is it a GUID
 			} else if (is_numeric($guid)) {
+				// $guid is a GUID so load
 				if (!$this->load($guid)) {
 					throw new IOException(elgg_echo('IOException:FailedToLoadGUID', array(get_class(), $guid)));
 				}
@@ -110,7 +107,7 @@ class ElggObject extends ElggEntity {
 
 		$this->attributes = $attrs;
 		$this->attributes['tables_loaded'] = 2;
-		cache_entity($this);
+		_elgg_cache_entity($this);
 
 		return true;
 	}
@@ -129,8 +126,12 @@ class ElggObject extends ElggEntity {
 		}
 
 		// Save ElggObject-specific attributes
-		return create_object_entity($this->get('guid'), $this->get('title'),
-			$this->get('description'));
+
+		_elgg_disable_caching_for_entity($this->guid);
+		$ret = create_object_entity($this->get('guid'), $this->get('title'), $this->get('description'));
+		_elgg_enable_caching_for_entity($this->guid);
+
+		return $ret;
 	}
 
 	/**
diff --git a/engine/classes/ElggPlugin.php b/engine/classes/ElggPlugin.php
index 8f71b79a8..545b9a53c 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) {
@@ -299,17 +299,15 @@ class ElggPlugin extends ElggObject {
 
 		$private_settings = get_data($q);
 
-		if ($private_settings) {
-			$return = array();
+		$return = array();
 
+		if ($private_settings) {
 			foreach ($private_settings as $setting) {
 				$return[$setting->name] = $setting->value;
 			}
-
-			return $return;
 		}
 
-		return false;
+		return $return;
 	}
 
 	/**
@@ -350,11 +348,14 @@ class ElggPlugin extends ElggObject {
 	 */
 	public function unsetAllSettings() {
 		$db_prefix = get_config('dbprefix');
-		$ps_prefix = elgg_namespace_plugin_private_setting('setting', '');
+
+		$us_prefix = elgg_namespace_plugin_private_setting('user_setting', '', $this->getID());
+		$is_prefix = elgg_namespace_plugin_private_setting('internal', '', $this->getID());
 
 		$q = "DELETE FROM {$db_prefix}private_settings
 			WHERE entity_guid = $this->guid
-			AND name NOT LIKE '$ps_prefix%'";
+			AND name NOT LIKE '$us_prefix%'
+			AND name NOT LIKE '$is_prefix%'";
 
 		return delete_data($q);
 	}
@@ -420,20 +421,18 @@ class ElggPlugin extends ElggObject {
 
 		$private_settings = get_data($q);
 
-		if ($private_settings) {
-			$return = array();
+		$return = array();
 
+		if ($private_settings) {
 			foreach ($private_settings as $setting) {
 				$name = substr($setting->name, $ps_prefix_len);
 				$value = $setting->value;
 
 				$return[$name] = $value;
 			}
-
-			return $return;
 		}
 
-		return false;
+		return $return;
 	}
 
 	/**
@@ -546,7 +545,7 @@ class ElggPlugin extends ElggObject {
 	 * Returns if the plugin is complete, meaning has all required files
 	 * and Elgg can read them and they make sense.
 	 *
-	 * @todo bad name? This could be confused with isValid() from ElggPackage.
+	 * @todo bad name? This could be confused with isValid() from ElggPluginPackage.
 	 *
 	 * @return bool
 	 */
@@ -597,6 +596,8 @@ 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 $site_guid Optional site guid
 	 * @return bool
 	 */
@@ -647,8 +648,8 @@ class ElggPlugin extends ElggObject {
 			// Note: this will not run re-run the init hooks!
 			if ($return) {
 				if ($this->canReadFile('activate.php')) {
-					$flags = ELGG_PLUGIN_INCLUDE_START | ELGG_PLUGIN_REGISTER_CLASSES
-							| ELGG_PLUGIN_REGISTER_LANGUAGES | ELGG_PLUGIN_REGISTER_VIEWS;
+					$flags = ELGG_PLUGIN_INCLUDE_START | ELGG_PLUGIN_REGISTER_CLASSES |
+							ELGG_PLUGIN_REGISTER_LANGUAGES | ELGG_PLUGIN_REGISTER_VIEWS;
 
 					$this->start($flags);
 
diff --git a/engine/classes/ElggPluginPackage.php b/engine/classes/ElggPluginPackage.php
index 2dc4bdb3d..37eb4bf4d 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();
@@ -294,6 +294,7 @@ class ElggPluginPackage {
 			return true;
 		}
 
+		$this->errorMsg = elgg_echo('unknown_error');
 		return false;
 	}
 
@@ -330,8 +331,10 @@ 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 +371,7 @@ 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..416df885c 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) {
@@ -351,7 +354,12 @@ class ElggPriorityList
 		return ($key !== NULL && $key !== FALSE);
 	}
 
-	// Countable
+	/**
+	 * Countable interface
+	 *
+	 * @see Countable::count()
+	 * @return int
+	 */
 	public function count() {
 		return count($this->elements);
 	}
diff --git a/engine/classes/ElggRelationship.php b/engine/classes/ElggRelationship.php
index efc0f7eff..d2e88882a 100644
--- a/engine/classes/ElggRelationship.php
+++ b/engine/classes/ElggRelationship.php
@@ -71,6 +71,7 @@ class ElggRelationship extends ElggData implements
 	 * Save the relationship
 	 *
 	 * @return int the relationship id
+	 * @throws IOException
 	 */
 	public function save() {
 		if ($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..dd996fe98 100644
--- a/engine/classes/ElggSite.php
+++ b/engine/classes/ElggSite.php
@@ -77,28 +77,24 @@ class ElggSite extends ElggEntity {
 					$msg = elgg_echo('IOException:FailedToLoadGUID', array(get_class(), $guid->guid));
 					throw new IOException($msg);
 				}
-
-			// Is $guid is an ElggSite? Use a copy constructor
 			} else if ($guid instanceof ElggSite) {
+				// $guid is an ElggSite so this is a copy constructor
 				elgg_deprecated_notice('This type of usage of the ElggSite constructor was deprecated. Please use the clone method.', 1.7);
 
 				foreach ($guid->attributes as $key => $value) {
 					$this->attributes[$key] = $value;
 				}
-
-			// Is this is an ElggEntity but not an ElggSite = ERROR!
 			} else if ($guid instanceof ElggEntity) {
+				// @todo remove and just use else clause
 				throw new InvalidParameterException(elgg_echo('InvalidParameterException:NonElggSite'));
-
-			// See if this is a URL
 			} else if (strpos($guid, "http") !== false) {
+				// url so retrieve by url
 				$guid = get_site_by_url($guid);
 				foreach ($guid->attributes as $key => $value) {
 					$this->attributes[$key] = $value;
 				}
-
-			// Is it a GUID
 			} else if (is_numeric($guid)) {
+				// $guid is a GUID so load
 				if (!$this->load($guid)) {
 					throw new IOException(elgg_echo('IOException:FailedToLoadGUID', array(get_class(), $guid)));
 				}
@@ -128,7 +124,7 @@ class ElggSite extends ElggEntity {
 
 		$this->attributes = $attrs;
 		$this->attributes['tables_loaded'] = 2;
-		cache_entity($this);
+		_elgg_cache_entity($this);
 
 		return true;
 	}
@@ -381,7 +377,9 @@ 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 +441,6 @@ 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/ElggStaticVariableCache.php b/engine/classes/ElggStaticVariableCache.php
index 17d849400..9c14fdfba 100644
--- a/engine/classes/ElggStaticVariableCache.php
+++ b/engine/classes/ElggStaticVariableCache.php
@@ -11,7 +11,7 @@ class ElggStaticVariableCache extends ElggSharedMemoryCache {
 	/**
 	 * The cache.
 	 *
-	 * @var unknown_type
+	 * @var array
 	 */
 	private static $__cache;
 
@@ -22,7 +22,7 @@ class ElggStaticVariableCache extends ElggSharedMemoryCache {
 	 * memory, optionally with a given namespace (to avoid overlap).
 	 *
 	 * @param string $namespace The namespace for this cache to write to.
-	 * @note namespaces of the same name are shared!
+	 * @warning namespaces of the same name are shared!
 	 */
 	function __construct($namespace = 'default') {
 		$this->setNamespace($namespace);
@@ -80,7 +80,7 @@ class ElggStaticVariableCache extends ElggSharedMemoryCache {
 	}
 
 	/**
-	 * This was probably meant to delete everything?
+	 * Clears the cache for a particular namespace
 	 *
 	 * @return void
 	 */
diff --git a/engine/classes/ElggTranslit.php b/engine/classes/ElggTranslit.php
index 676c59fc8..b4bf87797 100644
--- a/engine/classes/ElggTranslit.php
+++ b/engine/classes/ElggTranslit.php
@@ -20,11 +20,10 @@
  * and is licensed under the LGPL. For more information, see
  * <http://www.doctrine-project.org>.
  *
- * @author      Konsta Vesterinen <kvesteri@cc.hut.fi>
- * @author      Jonathan H. Wage <jonwage@gmail.com>
- *
- * @author      Steve Clay <steve@mrclay.org>
- * @package     Elgg.Core
+ * @package Elgg.Core
+ * @author  Konsta Vesterinen <kvesteri@cc.hut.fi>
+ * @author  Jonathan H. Wage <jonwage@gmail.com>
+ * @author  Steve Clay <steve@mrclay.org>
  *
  * @access private Plugin authors should not use this directly
  */
@@ -32,8 +31,9 @@ class ElggTranslit {
 
 	/**
 	 * Create a version of a string for embedding in a URL
-	 * @param string $string a UTF-8 string
-	 * @param string $separator
+	 *
+	 * @param string $string    A UTF-8 string
+	 * @param string $separator The character to separate words with
 	 * @return string
 	 */
 	static public function urlize($string, $separator = '-') {
@@ -49,24 +49,29 @@ class ElggTranslit {
 		// Internationalization, AND 日本語!
 		$string = self::transliterateAscii($string);
 
-		// more translation
+		// allow HTML tags in titles
+		$string = preg_replace('~<([a-zA-Z][^>]*)>~', ' $1 ', $string);
+
+		// more substitutions
+		// @todo put these somewhere else
 		$string = strtr($string, array(
-			// Euro/GBP
-			"\xE2\x82\xAC" /* € */ => 'E', "\xC2\xA3" /* £ */ => 'GBP',
+			// currency
+			"\xE2\x82\xAC" /* € */ => ' E ',
+			"\xC2\xA3" /* £ */ => ' GBP ',
 		));
 
 		// remove all ASCII except 0-9a-zA-Z, hyphen, underscore, and whitespace
 		// note: "x" modifier did not work with this pattern.
 		$string = preg_replace('~['
-			. '\x00-\x08'  # control chars
-			. '\x0b\x0c'   # vert tab, form feed
-			. '\x0e-\x1f'  # control chars
-			. '\x21-\x2c'  # ! ... ,
-			. '\x2e\x2f'   # . slash
-			. '\x3a-\x40'  # : ... @
-			. '\x5b-\x5e'  # [ ... ^
-			. '\x60'       # `
-			. '\x7b-\x7f'  # { ... DEL
+			. '\x00-\x08'  // control chars
+			. '\x0b\x0c'   // vert tab, form feed
+			. '\x0e-\x1f'  // control chars
+			. '\x21-\x2c'  // ! ... ,
+			. '\x2e\x2f'   // . slash
+			. '\x3a-\x40'  // : ... @
+			. '\x5b-\x5e'  // [ ... ^
+			. '\x60'       // `
+			. '\x7b-\x7f'  // { ... DEL
 			. ']~', '', $string);
 		$string = strtr($string, '', '');
 
@@ -80,10 +85,10 @@ class ElggTranslit {
 		// note: we cannot use [^0-9a-zA-Z] because that matches multibyte chars.
 		// note: "x" modifier did not work with this pattern.
 		$pattern = '~['
-			. '\x00-\x2f'  # controls ... slash
-			. '\x3a-\x40'  # : ... @
-			. '\x5b-\x60'  # [ ... `
-			. '\x7b-\x7f'  # { ... DEL
+			. '\x00-\x2f'  // controls ... slash
+			. '\x3a-\x40'  // : ... @
+			. '\x5b-\x60'  // [ ... `
+			. '\x7b-\x7f'  // { ... DEL
 			. ']+~x';
 
 		// ['internationalization', 'and', '日本語']
@@ -98,6 +103,7 @@ class ElggTranslit {
 
 	/**
 	 * Transliterate Western multibyte chars to ASCII
+	 *
 	 * @param string $utf8 a UTF-8 string
 	 * @return string
 	 */
@@ -247,6 +253,7 @@ class ElggTranslit {
 
 	/**
 	 * Tests that "normalizer_normalize" exists and works
+	 *
 	 * @return bool
 	 */
 	static public function hasNormalizerSupport() {
@@ -255,7 +262,7 @@ class ElggTranslit {
 			$form_c = "\xC3\x85"; // 'LATIN CAPITAL LETTER A WITH RING ABOVE' (U+00C5)
 			$form_d = "A\xCC\x8A"; // A followed by 'COMBINING RING ABOVE' (U+030A)
 			$ret = (function_exists('normalizer_normalize')
-				    && $form_c === normalizer_normalize($form_d));
+				&& $form_c === normalizer_normalize($form_d));
 		}
 		return $ret;
 	}
diff --git a/engine/classes/ElggUser.php b/engine/classes/ElggUser.php
index 6c1cdc1de..6163f9b62 100644
--- a/engine/classes/ElggUser.php
+++ b/engine/classes/ElggUser.php
@@ -40,6 +40,9 @@ class ElggUser extends ElggEntity
 		$this->attributes['code'] = NULL;
 		$this->attributes['banned'] = "no";
 		$this->attributes['admin'] = 'no';
+		$this->attributes['prev_last_action'] = NULL;
+		$this->attributes['last_login'] = NULL;
+		$this->attributes['prev_last_login'] = NULL;
 		$this->attributes['tables_split'] = 2;
 	}
 
@@ -65,30 +68,26 @@ class ElggUser extends ElggEntity
 					$msg = elgg_echo('IOException:FailedToLoadGUID', array(get_class(), $guid->guid));
 					throw new IOException($msg);
 				}
-
-			// See if this is a username
 			} else if (is_string($guid)) {
+				// $guid is a username
 				$user = get_user_by_username($guid);
 				if ($user) {
 					foreach ($user->attributes as $key => $value) {
 						$this->attributes[$key] = $value;
 					}
 				}
-
-			// Is $guid is an ElggUser? Use a copy constructor
 			} else if ($guid instanceof ElggUser) {
+				// $guid is an ElggUser so this is a copy constructor
 				elgg_deprecated_notice('This type of usage of the ElggUser constructor was deprecated. Please use the clone method.', 1.7);
 
 				foreach ($guid->attributes as $key => $value) {
 					$this->attributes[$key] = $value;
 				}
-
-			// Is this is an ElggEntity but not an ElggUser = ERROR!
 			} else if ($guid instanceof ElggEntity) {
+				// @todo why have a special case here
 				throw new InvalidParameterException(elgg_echo('InvalidParameterException:NonElggUser'));
-
-			// Is it a GUID
 			} else if (is_numeric($guid)) {
+				// $guid is a GUID so load entity
 				if (!$this->load($guid)) {
 					throw new IOException(elgg_echo('IOException:FailedToLoadGUID', array(get_class(), $guid)));
 				}
@@ -116,7 +115,7 @@ class ElggUser extends ElggEntity
 
 		$this->attributes = $attrs;
 		$this->attributes['tables_loaded'] = 2;
-		cache_entity($this);
+		_elgg_cache_entity($this);
 
 		return true;
 	}
@@ -133,9 +132,13 @@ class ElggUser extends ElggEntity
 		}
 
 		// Now save specific stuff
-		return create_user_entity($this->get('guid'), $this->get('name'), $this->get('username'),
+		_elgg_disable_caching_for_entity($this->guid);
+		$ret = create_user_entity($this->get('guid'), $this->get('name'), $this->get('username'),
 			$this->get('password'), $this->get('salt'), $this->get('email'), $this->get('language'),
 			$this->get('code'));
+		_elgg_enable_caching_for_entity($this->guid);
+
+		return $ret;
 	}
 
 	/**
diff --git a/engine/classes/ElggVolatileMetadataCache.php b/engine/classes/ElggVolatileMetadataCache.php
index 8a33c198d..4acda7cee 100644
--- a/engine/classes/ElggVolatileMetadataCache.php
+++ b/engine/classes/ElggVolatileMetadataCache.php
@@ -33,9 +33,11 @@ class ElggVolatileMetadataCache {
 	protected $ignoreAccess = null;
 
 	/**
-	 * @param int $entity_guid
-	 *
-	 * @param array $values
+	 * Cache metadata for an entity
+	 * 
+	 * @param int   $entity_guid The GUID of the entity
+	 * @param array $values      The metadata values to cache
+	 * @return void
 	 */
 	public function saveAll($entity_guid, array $values) {
 		if (!$this->getIgnoreAccess()) {
@@ -45,8 +47,9 @@ class ElggVolatileMetadataCache {
 	}
 
 	/**
-	 * @param int $entity_guid
-	 *
+	 * Get the metadata for an entity
+	 * 
+	 * @param int $entity_guid The GUID of the entity
 	 * @return array
 	 */
 	public function loadAll($entity_guid) {
@@ -61,15 +64,17 @@ class ElggVolatileMetadataCache {
 	 * Declare that there may be fetch-able metadata names in storage that this
 	 * cache doesn't know about
 	 *
-	 * @param int $entity_guid
+	 * @param int $entity_guid The GUID of the entity
+	 * @return void
 	 */
 	public function markOutOfSync($entity_guid) {
 		unset($this->isSynchronized[$entity_guid]);
 	}
 
 	/**
-	 * @param $entity_guid
-	 *
+	 * Have all the metadata for this entity been cached?
+	 * 
+	 * @param int $entity_guid The GUID of the entity
 	 * @return bool
 	 */
 	public function isSynchronized($entity_guid) {
@@ -77,13 +82,15 @@ class ElggVolatileMetadataCache {
 	}
 
 	/**
-	 * @param int $entity_guid
-	 *
-	 * @param string $name
-	 *
-	 * @param array|int|string|null $value  null means it is known that there is no
-	 *                                      fetch-able metadata under this name
-	 * @param bool $allow_multiple
+	 * Cache a piece of metadata
+	 * 
+	 * @param int                   $entity_guid    The GUID of the entity
+	 * @param string                $name           The metadata name
+	 * @param array|int|string|null $value          The metadata value. null means it is 
+	 *                                              known that there is no fetch-able 
+	 *                                              metadata under this name
+	 * @param bool                  $allow_multiple Can the metadata be an array
+	 * @return void
 	 */
 	public function save($entity_guid, $name, $value, $allow_multiple = false) {
 		if ($this->getIgnoreAccess()) {
@@ -115,10 +122,8 @@ class ElggVolatileMetadataCache {
 	 * function's return value should be trusted (otherwise a null return value
 	 * is ambiguous).
 	 *
-	 * @param int $entity_guid
-	 *
-	 * @param string $name
-	 *
+	 * @param int    $entity_guid The GUID of the entity
+	 * @param string $name        The metadata name
 	 * @return array|string|int|null null = value does not exist
 	 */
 	public function load($entity_guid, $name) {
@@ -133,9 +138,9 @@ class ElggVolatileMetadataCache {
 	 * Forget about this metadata entry. We don't want to try to guess what the
 	 * next fetch from storage will return
 	 *
-	 * @param int $entity_guid
-	 *
-	 * @param string $name
+	 * @param int    $entity_guid The GUID of the entity
+	 * @param string $name        The metadata name
+	 * @return void
 	 */
 	public function markUnknown($entity_guid, $name) {
 		unset($this->values[$entity_guid][$name]);
@@ -145,10 +150,8 @@ class ElggVolatileMetadataCache {
 	/**
 	 * If true, load() will return an accurate value for this name
 	 *
-	 * @param int $entity_guid
-	 *
-	 * @param string $name
-	 *
+	 * @param int    $entity_guid The GUID of the entity
+	 * @param string $name        The metadata name
 	 * @return bool
 	 */
 	public function isKnown($entity_guid, $name) {
@@ -163,10 +166,8 @@ class ElggVolatileMetadataCache {
 	/**
 	 * Declare that metadata under this name is known to be not fetch-able from storage
 	 *
-	 * @param int $entity_guid
-	 *
-	 * @param string $name
-	 *
+	 * @param int    $entity_guid The GUID of the entity
+	 * @param string $name        The metadata name
 	 * @return array
 	 */
 	public function markEmpty($entity_guid, $name) {
@@ -176,7 +177,8 @@ class ElggVolatileMetadataCache {
 	/**
 	 * Forget about all metadata for an entity
 	 *
-	 * @param int $entity_guid
+	 * @param int $entity_guid The GUID of the entity
+	 * @return void
 	 */
 	public function clear($entity_guid) {
 		$this->values[$entity_guid] = array();
@@ -185,6 +187,8 @@ class ElggVolatileMetadataCache {
 
 	/**
 	 * Clear entire cache and mark all entities as out of sync
+	 * 
+	 * @return void
 	 */
 	public function flush() {
 		$this->values = array();
@@ -197,7 +201,8 @@ class ElggVolatileMetadataCache {
 	 *
 	 * This setting makes this component a little more loosely-coupled.
 	 *
-	 * @param bool $ignore
+	 * @param bool $ignore Whether to ignore access or not
+	 * @return void
 	 */
 	public function setIgnoreAccess($ignore) {
 		$this->ignoreAccess = (bool) $ignore;
@@ -205,12 +210,16 @@ class ElggVolatileMetadataCache {
 
 	/**
 	 * Tell the cache to call elgg_get_ignore_access() to determing access status.
+	 * 
+	 * @return void
 	 */
 	public function unsetIgnoreAccess() {
 		$this->ignoreAccess = null;
 	}
 
 	/**
+	 * Get the ignore access value
+	 * 
 	 * @return bool
 	 */
 	protected function getIgnoreAccess() {
@@ -225,12 +234,10 @@ class ElggVolatileMetadataCache {
 	 * Invalidate based on options passed to the global *_metadata functions
 	 *
 	 * @param string $action  Action performed on metadata. "delete", "disable", or "enable"
-	 *
-	 * @param array $options  Options passed to elgg_(delete|disable|enable)_metadata
-	 *
-	 *   "guid" if given, invalidation will be limited to this entity
-	 *
-	 *   "metadata_name" if given, invalidation will be limited to metadata with this name
+	 * @param array  $options Options passed to elgg_(delete|disable|enable)_metadata
+	 *                         "guid" if given, invalidation will be limited to this entity
+	 *                         "metadata_name" if given, invalidation will be limited to metadata with this name
+	 * @return void
 	 */
 	public function invalidateByOptions($action, array $options) {
 		// remove as little as possible, optimizing for common cases
@@ -254,7 +261,10 @@ class ElggVolatileMetadataCache {
 	}
 
 	/**
-	 * @param int|array $guids
+	 * Populate the cache from a set of entities
+	 * 
+	 * @param int|array $guids Array of or single GUIDs
+	 * @return void
 	 */
 	public function populateFromEntities($guids) {
 		if (empty($guids)) {
@@ -318,9 +328,7 @@ class ElggVolatileMetadataCache {
 	 * cache if RAM usage becomes an issue.
 	 *
 	 * @param array $guids GUIDs of entities to examine
-	 *
-	 * @param int $limit Limit in characters of all metadata (with ints casted to strings)
-	 *
+	 * @param int   $limit Limit in characters of all metadata (with ints casted to strings)
 	 * @return array
 	 */
 	public function filterMetadataHeavyEntities(array $guids, $limit = 1024000) {
diff --git a/engine/classes/ElggWidget.php b/engine/classes/ElggWidget.php
index 99708f66a..66191bf47 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 {
 
@@ -141,10 +146,15 @@ class ElggWidget extends ElggObject {
 			}
 		}
 
+		$bottom_rank = count($widgets);
+		if ($column == $this->column) {
+			$bottom_rank--;
+		}
+		
 		if ($rank == 0) {
 			// top of the column
 			$this->order = reset($widgets)->order - 10;
-		} elseif ($rank == (count($widgets) - 1)) {
+		} elseif ($rank == $bottom_rank) {
 			// bottom of the column of active widgets
 			$this->order = end($widgets)->order + 10;
 		} else {
diff --git a/engine/classes/ElggXMLElement.php b/engine/classes/ElggXMLElement.php
index 65a13912c..cbd3fc5ce 100644
--- a/engine/classes/ElggXMLElement.php
+++ b/engine/classes/ElggXMLElement.php
@@ -20,7 +20,12 @@ class ElggXMLElement {
 		if ($xml instanceof SimpleXMLElement) {
 			$this->_element = $xml;
 		} else {
+			// do not load entities
+			$disable_load_entities = libxml_disable_entity_loader(true);
+
 			$this->_element = new SimpleXMLElement($xml);
+
+			libxml_disable_entity_loader($disable_load_entities);
 		}
 	}
 
@@ -32,7 +37,7 @@ class ElggXMLElement {
 	}
 
 	/**
-	 * @return array:string The attributes
+	 * @return string[] The attributes
 	 */
 	public function getAttributes() {
 		//include namespace declarations as attributes
@@ -64,7 +69,7 @@ class ElggXMLElement {
 	}
 
 	/**
-	 * @return array:ElggXMLElement Child elements
+	 * @return ElggXMLElement[] Child elements
 	 */
 	public function getChildren() {
 		$children = $this->_element->children();
@@ -76,6 +81,12 @@ class ElggXMLElement {
 		return $result;
 	}
 
+	/**
+	 * Override ->
+	 * 
+	 * @param string $name Property name
+	 * @return mixed
+	 */
 	function __get($name) {
 		switch ($name) {
 			case 'name':
@@ -94,6 +105,12 @@ class ElggXMLElement {
 		return null;
 	}
 
+	/**
+	 * Override isset
+	 * 
+	 * @param string $name Property name
+	 * @return boolean
+	 */
 	function __isset($name) {
 		switch ($name) {
 			case 'name':
@@ -111,5 +128,4 @@ class ElggXMLElement {
 		}
 		return false;
 	}
-
-}
\ No newline at end of file
+}
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, $uuid2) {
 		parent::__construct();
@@ -25,7 +25,7 @@ class ODDRelationship extends ODD {
 	/**
 	 * Returns 'relationship'
 	 *
-	 * @return 'relationship'
+	 * @return string 'relationship'
 	 */
 	protected function getTagName() {
 		return "relationship";
diff --git a/engine/handlers/cache_handler.php b/engine/handlers/cache_handler.php
index 7706c2c92..36fc665bb 100644
--- a/engine/handlers/cache_handler.php
+++ b/engine/handlers/cache_handler.php
@@ -88,15 +88,18 @@ header("ETag: \"$etag\"");
 $filename = $dataroot . 'views_simplecache/' . md5($viewtype . $view);
 
 if (file_exists($filename)) {
-	$contents = file_get_contents($filename);
+	readfile($filename);
 } else {
 	// someone trying to access a non-cached file or a race condition with cache flushing
 	mysql_close($mysql_dblink);
 	require_once(dirname(dirname(__FILE__)) . "/start.php");
-	elgg_regenerate_simplecache();
+
+	global $CONFIG;
+	if (!in_array($view, $CONFIG->views->simplecache)) {
+		header("HTTP/1.1 404 Not Found");
+		exit;
+	}
 
 	elgg_set_viewtype($viewtype);
-	$contents = elgg_view($view);
+	echo elgg_view($view);
 }
-
-echo $contents;
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, $params) {
diff --git a/engine/lib/actions.php b/engine/lib/actions.php
index 53b185dea..8047914ac 100644
--- a/engine/lib/actions.php
+++ b/engine/lib/actions.php
@@ -65,18 +65,16 @@ function action($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',
 	);
 
 	if (!in_array($action, $exceptions)) {
-		// All actions require a token.
-		action_gatekeeper();
+		action_gatekeeper($action);
 	}
 
 	$forwarder = str_replace(elgg_get_site_url(), "", $forwarder);
@@ -189,6 +187,26 @@ function elgg_unregister_action($action) {
 }
 
 /**
+ * Is the token timestamp within acceptable range?
+ * 
+ * @param int $ts timestamp from the CSRF token
+ * 
+ * @return bool
+ */
+function _elgg_validate_token_timestamp($ts) {
+	$action_token_timeout = elgg_get_config('action_token_timeout');
+	// default is 2 hours
+	$timeout = ($action_token_timeout !== null) ? $action_token_timeout : 2;
+
+	$hour = 60 * 60;
+	$timeout = $timeout * $hour;
+	$now = time();
+
+	// Validate time to ensure its not crazy
+	return ($timeout == 0 || ($ts > $now - $timeout) && ($ts < $now + $timeout));
+}
+
+/**
  * Validate an action token.
  *
  * Calls to actions will automatically validate tokens. If tokens are not
@@ -206,8 +224,6 @@ function elgg_unregister_action($action) {
  * @access private
  */
 function validate_action_token($visibleerrors = TRUE, $token = NULL, $ts = NULL) {
-	global $CONFIG;
-
 	if (!$token) {
 		$token = get_input('__elgg_token');
 	}
@@ -216,29 +232,18 @@ function validate_action_token($visibleerrors = TRUE, $token = NULL, $ts = NULL)
 		$ts = get_input('__elgg_ts');
 	}
 
-	if (!isset($CONFIG->action_token_timeout)) {
-		// default to 2 hours
-		$timeout = 2;
-	} else {
-		$timeout = $CONFIG->action_token_timeout;
-	}
-
 	$session_id = session_id();
 
 	if (($token) && ($ts) && ($session_id)) {
 		// generate token, check with input and forward if invalid
-		$generated_token = generate_action_token($ts);
+		$required_token = generate_action_token($ts);
 
 		// Validate token
-		if ($token == $generated_token) {
-			$hour = 60 * 60;
-			$timeout = $timeout * $hour;
-			$now = time();
-
-			// Validate time to ensure its not crazy
-			if ($timeout == 0 || ($ts > $now - $timeout) && ($ts < $now + $timeout)) {
+		if ($token == $required_token) {
+			
+			if (_elgg_validate_token_timestamp($ts)) {
 				// We have already got this far, so unless anything
-				// else says something to the contry we assume we're ok
+				// else says something to the contrary we assume we're ok
 				$returnval = true;
 
 				$returnval = elgg_trigger_plugin_hook('action_gatekeeper:permissions:check', 'all', array(
@@ -252,10 +257,20 @@ function validate_action_token($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($_POST)) {
@@ -284,12 +299,33 @@ function validate_action_token($visibleerrors = TRUE, $token = NULL, $ts = NULL)
  * This function verifies form input for security features (like a generated token),
  * and forwards if they are invalid.
  *
+ * @param string $action The action being performed
+ * 
  * @return mixed True if valid or redirects.
  * @access private
  */
-function action_gatekeeper() {
-	if (validate_action_token()) {
-		return TRUE;
+function action_gatekeeper($action) {
+	if ($action === 'login') {
+		if (validate_action_token(false)) {
+			return true;
+		}
+		
+		$token = get_input('__elgg_token');
+		$ts = (int)get_input('__elgg_ts');
+		if ($token && _elgg_validate_token_timestamp($ts)) {
+			// The tokens are present and the time looks valid: this is probably a mismatch due to the 
+			// login form being on a different domain.
+			register_error(elgg_echo('actiongatekeeper:crosssitelogin'));
+			
+			
+			forward('login', 'csrf');
+		}
+		
+		// let the validator send an appropriate msg
+		validate_action_token();
+		
+	} elseif (validate_action_token()) {
+		return true;
 	}
 
 	forward(REFERER, 'csrf');
@@ -328,16 +364,19 @@ function generate_action_token($timestamp) {
 }
 
 /**
- * Initialise the site secret hash.
+ * Initialise the site secret (32 bytes: "z" to indicate format + 186-bit key in Base64 URL).
  *
  * Used during installation and saves as a datalist.
  *
+ * Note: Old secrets were hex encoded.
+ *
  * @return mixed The site secret hash or false
  * @access private
  * @todo Move to better file.
  */
 function init_site_secret() {
-	$secret = md5(rand() . microtime());
+	$secret = 'z' . ElggCrypto::getRandomString(31);
+
 	if (datalist_set('__site_secret__', $secret)) {
 		return $secret;
 	}
@@ -364,6 +403,26 @@ function get_site_secret() {
 }
 
 /**
+ * Get the strength of the site secret
+ *
+ * @return string "strong", "moderate", or "weak"
+ * @access private
+ */
+function _elgg_get_site_secret_strength() {
+	$secret = get_site_secret();
+	if ($secret[0] !== 'z') {
+		$rand_max = getrandmax();
+		if ($rand_max < pow(2, 16)) {
+			return 'weak';
+		}
+		if ($rand_max < pow(2, 32)) {
+			return 'moderate';
+		}
+	}
+	return 'strong';
+}
+
+/**
  * Check if an action is registered and its script exists.
  *
  * @param string $action Action name
diff --git a/engine/lib/admin.php b/engine/lib/admin.php
index 35ab5599d..f36f29668 100644
--- a/engine/lib/admin.php
+++ b/engine/lib/admin.php
@@ -134,11 +134,11 @@ function elgg_delete_admin_notice($id) {
 }
 
 /**
- * List all admin messages.
+ * Get admin notices. An admin must be logged in since the notices are private.
  *
  * @param int $limit Limit
  *
- * @return array List of admin notices
+ * @return array Array of admin notices
  * @since 1.8.0
  */
 function elgg_get_admin_notices($limit = 10) {
@@ -158,11 +158,13 @@ function elgg_get_admin_notices($limit = 10) {
  * @since 1.8.0
  */
 function elgg_admin_notice_exists($id) {
+	$old_ia = elgg_set_ignore_access(true);
 	$notice = elgg_get_entities_from_metadata(array(
 		'type' => 'object',
 		'subtype' => 'admin_notice',
 		'metadata_name_value_pair' => array('name' => 'admin_notice_id', 'value' => $id)
 	));
+	elgg_set_ignore_access($old_ia);
 
 	return ($notice) ? TRUE : FALSE;
 }
@@ -234,6 +236,7 @@ function admin_init() {
 	elgg_register_action('admin/site/update_advanced', '', 'admin');
 	elgg_register_action('admin/site/flush_cache', '', 'admin');
 	elgg_register_action('admin/site/unlock_upgrade', '', 'admin');
+	elgg_register_action('admin/site/regenerate_secret', '', 'admin');
 
 	elgg_register_action('admin/menu/save', '', 'admin');
 
@@ -289,6 +292,7 @@ function admin_init() {
 	elgg_register_admin_menu_item('configure', 'settings', null, 100);
 	elgg_register_admin_menu_item('configure', 'basic', 'settings', 10);
 	elgg_register_admin_menu_item('configure', 'advanced', 'settings', 20);
+	elgg_register_admin_menu_item('configure', 'advanced/site_secret', 'settings', 25);
 	elgg_register_admin_menu_item('configure', 'menu_items', 'appearance', 30);
 	elgg_register_admin_menu_item('configure', 'profile_fields', 'appearance', 40);
 	// default widgets is added via an event handler elgg_default_widgets_init() in widgets.php
@@ -346,7 +350,7 @@ 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 $plugin) {
@@ -380,6 +384,7 @@ function elgg_admin_add_plugin_settings_menu() {
  */
 function elgg_admin_sort_page_menu($hook, $type, $return, $params) {
 	$configure_items = $return['configure'];
+	/* @var ElggMenuItem[] $configure_items */
 	foreach ($configure_items as $menu_item) {
 		if ($menu_item->getName() == 'settings') {
 			$settings = $menu_item;
@@ -387,6 +392,7 @@ function elgg_admin_sort_page_menu($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($children, array('ElggMenuBuilder', 'compareByText'));
@@ -466,14 +472,18 @@ function admin_page_handler($page) {
 	$vars = array('page' => $page);
 
 	// special page for plugin settings since we create the form for them
-	if ($page[0] == 'plugin_settings' && isset($page[1]) &&
-		(elgg_view_exists("settings/{$page[1]}/edit") || elgg_view_exists("plugins/{$page[1]}/settings"))) {
+	if ($page[0] == 'plugin_settings') {
+		if (isset($page[1]) && (elgg_view_exists("settings/{$page[1]}/edit") || 
+			elgg_view_exists("plugins/{$page[1]}/settings"))) {
 
-		$view = 'admin/plugin_settings';
-		$plugin = elgg_get_plugin_from_id($page[1]);
-		$vars['plugin'] = $plugin;
+			$view = 'admin/plugin_settings';
+			$plugin = elgg_get_plugin_from_id($page[1]);
+			$vars['plugin'] = $plugin;
 
-		$title = elgg_echo("admin:{$page[0]}");
+			$title = elgg_echo("admin:{$page[0]}");
+		} else {
+			forward('', '404');
+		}
 	} else {
 		$view = 'admin/' . implode('/', $page);
 		$title = elgg_echo("admin:{$page[0]}");
@@ -552,7 +562,7 @@ function admin_plugin_screenshot_page_handler($pages) {
  *	* COPYRIGHT.txt
  *	* LICENSE.txt
  *
- * @param type $page
+ * @param array $pages
  * @return bool
  * @access private
  */
@@ -615,7 +625,11 @@ function admin_markdown_page_handler($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, $user) {
@@ -637,6 +651,7 @@ function elgg_add_admin_widgets($event, $type, $user) {
 			$guid = elgg_create_widget($user->getGUID(), $handler, 'admin');
 			if ($guid) {
 				$widget = get_entity($guid);
+				/* @var ElggWidget $widget */
 				$widget->move($column, $position);
 			}
 		}
diff --git a/engine/lib/annotations.php b/engine/lib/annotations.php
index 3b9f84703..5e9b530de 100644
--- a/engine/lib/annotations.php
+++ b/engine/lib/annotations.php
@@ -17,6 +17,7 @@
  */
 function row_to_elggannotation($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);
 }
@@ -211,7 +224,7 @@ function elgg_get_annotations(array $options = array()) {
  *          annotation_name(s), annotation_value(s), or guid(s) must be set.
  *
  * @param array $options An options array. {@See elgg_get_annotations()}
- * @return mixed Null if the metadata name is invalid. Bool on success or fail.
+ * @return bool|null true on success, false on failure, null if no annotations to delete.
  * @since 1.8.0
  */
 function elgg_delete_annotations(array $options) {
@@ -229,16 +242,20 @@ function elgg_delete_annotations(array $options) {
  * @warning Unlike elgg_get_annotations() this will not accept an empty options array!
  *
  * @param array $options An options array. {@See elgg_get_annotations()}
- * @return mixed
+ * @return bool|null true on success, false on failure, null if no annotations disabled.
  * @since 1.8.0
  */
 function elgg_disable_annotations(array $options) {
 	if (!elgg_is_valid_options_for_batch_operation($options, 'annotations')) {
 		return false;
 	}
+	
+	// if we can see hidden (disabled) we need to use the offset
+	// otherwise we risk an infinite loop if there are more than 50
+	$inc_offset = access_get_show_hidden_status();
 
 	$options['metastring_type'] = 'annotations';
-	return elgg_batch_metastring_based_objects($options, 'elgg_batch_disable_callback', false);
+	return elgg_batch_metastring_based_objects($options, 'elgg_batch_disable_callback', $inc_offset);
 }
 
 /**
@@ -246,8 +263,11 @@ function elgg_disable_annotations(array $options) {
  *
  * @warning Unlike elgg_get_annotations() this will not accept an empty options array!
  *
+ * @warning In order to enable annotations, you must first use
+ * {@link access_show_hidden_entities()}.
+ *
  * @param array $options An options array. {@See elgg_get_annotations()}
- * @return mixed
+ * @return bool|null true on success, false on failure, null if no metadata enabled.
  * @since 1.8.0
  */
 function elgg_enable_annotations(array $options) {
@@ -403,8 +423,8 @@ function elgg_list_entities_from_annotations($options = array()) {
 function elgg_get_entities_from_annotation_calculation($options) {
 	$db_prefix = elgg_get_config('dbprefix');
 	$defaults = array(
-		'calculation'	=>	'sum',
-		'order_by'		=>	'annotation_calculation desc'
+		'calculation' => 'sum',
+		'order_by' => 'annotation_calculation desc'
 	);
 
 	$options = array_merge($defaults, $options);
@@ -424,6 +444,10 @@ function elgg_get_entities_from_annotation_calculation($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);
 }
 
@@ -437,23 +461,30 @@ function elgg_get_entities_from_annotation_calculation($options) {
  * @return string
  */
 function elgg_list_entities_from_annotation_calculation($options) {
+	$defaults = array(
+		'calculation' => 'sum',
+		'order_by' => 'annotation_calculation desc'
+	);
+	$options = array_merge($defaults, $options);
+
 	return elgg_list_entities($options, 'elgg_get_entities_from_annotation_calculation');
 }
 
 /**
- * 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($params['guid']))) {
 		throw new InvalidParameterException(elgg_echo('InvalidParameterException:GUIDNotForExport'));
@@ -464,12 +495,12 @@ function export_annotation_plugin_hook($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 $r) {
@@ -514,15 +545,16 @@ function elgg_annotation_exists($entity_guid, $annotation_type, $owner_guid = NU
 		return FALSE;
 	}
 
-	$entity_guid = (int)$entity_guid;
-	$annotation_type = sanitise_string($annotation_type);
+	$entity_guid = sanitize_int($entity_guid);
+	$owner_guid = sanitize_int($owner_guid);
+	$annotation_type = sanitize_string($annotation_type);
 
-	$sql = "select a.id" .
-			" FROM {$CONFIG->dbprefix}annotations a, {$CONFIG->dbprefix}metastrings m " .
-			" WHERE a.owner_guid={$owner_guid} AND a.entity_guid={$entity_guid} " .
-			" AND a.name_id=m.id AND m.string='{$annotation_type}'";
+	$sql = "SELECT a.id FROM {$CONFIG->dbprefix}annotations a" .
+			" JOIN {$CONFIG->dbprefix}metastrings m ON a.name_id = m.id" .
+			" WHERE a.owner_guid = $owner_guid AND a.entity_guid = $entity_guid" .
+			" AND m.string = '$annotation_type'";
 
-	if ($check_annotation = get_data_row($sql)) {
+	if (get_data_row($sql)) {
 		return TRUE;
 	}
 
@@ -541,6 +573,7 @@ function elgg_comment_url_handler(ElggAnnotation $comment) {
 	if ($entity) {
 		return $entity->getURL() . '#item-annotation-' . $comment->id;
 	}
+	return "";
 }
 
 /**
@@ -557,6 +590,12 @@ 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, $params) {
diff --git a/engine/lib/cache.php b/engine/lib/cache.php
index be1c43e14..3116c1a9b 100644
--- a/engine/lib/cache.php
+++ b/engine/lib/cache.php
@@ -125,7 +125,7 @@ function elgg_get_filepath_cache() {
  * @access private
  */
 function elgg_filepath_cache_reset() {
-	return elgg_reset_system_cache();
+	elgg_reset_system_cache();
 }
 /**
  * @access private
@@ -143,13 +143,13 @@ function elgg_filepath_cache_load($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 */
@@ -208,6 +208,7 @@ function elgg_get_simplecache_url($type, $view) {
 	global $CONFIG;
 	$lastcache = (int)$CONFIG->lastcache;
 	$viewtype = elgg_get_viewtype();
+	elgg_register_simplecache_view("$type/$view");// see #5302
 	if (elgg_is_simplecache_enabled()) {
 		$url = elgg_get_site_url() . "cache/$type/$viewtype/$view.$lastcache.$type";
 	} else {
@@ -222,7 +223,7 @@ 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 $viewtype Optional viewtype to regenerate. Defaults to all valid viewtypes.
  *
@@ -444,7 +445,7 @@ function _elgg_cache_init() {
 	if ($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  $type           The type of entity (eg "user", "object" etc)
diff --git a/engine/lib/configuration.php b/engine/lib/configuration.php
index b10e51130..55e5bbd36 100644
--- a/engine/lib/configuration.php
+++ b/engine/lib/configuration.php
@@ -36,6 +36,7 @@ function elgg_get_site_url($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;
 	}
 
@@ -485,9 +486,9 @@ function get_config($name, $site_guid = 0) {
 	// @todo these haven't really been implemented in Elgg 1.8. Complete in 1.9.
 	// show dep message
 	if ($new_name) {
-	//	$msg = "Config value $name has been renamed as $new_name";
+		//	$msg = "Config value $name has been renamed as $new_name";
 		$name = $new_name;
-	//	elgg_deprecated_notice($msg, $dep_version);
+		//	elgg_deprecated_notice($msg, $dep_version);
 	}
 
 	// decide from where to return the value
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..a7949788d 100644
--- a/engine/lib/database.php
+++ b/engine/lib/database.php
@@ -12,15 +12,19 @@
 /**
  * Query cache for all queries.
  *
- * Each query and its results are stored in this array as:
+ * Each query and its results are stored in this cache as:
  * <code>
- * $DB_QUERY_CACHE[$query] => array(result1, result2, ... resultN)
+ * $DB_QUERY_CACHE[query hash] => array(result1, result2, ... resultN)
  * </code>
+ * @see elgg_query_runner() for details on the hash.
  *
- * @global array $DB_QUERY_CACHE
+ * @warning Elgg used to set this as an empty array to turn off the cache
+ *
+ * @global ElggLRUCache|null $DB_QUERY_CACHE
+ * @access private
  */
 global $DB_QUERY_CACHE;
-$DB_QUERY_CACHE = array();
+$DB_QUERY_CACHE = null;
 
 /**
  * Queries to be executed upon shutdown.
@@ -38,6 +42,7 @@ $DB_QUERY_CACHE = array();
  * </code>
  *
  * @global array $DB_DELAYED_QUERIES
+ * @access private
  */
 global $DB_DELAYED_QUERIES;
 $DB_DELAYED_QUERIES = array();
@@ -48,7 +53,8 @@ $DB_DELAYED_QUERIES = array();
  * Each database link created with establish_db_link($name) is stored in
  * $dblink as $dblink[$name] => resource.  Use get_db_link($name) to retrieve it.
  *
- * @global array $dblink
+ * @global resource[] $dblink
+ * @access private
  */
 global $dblink;
 $dblink = array();
@@ -59,6 +65,7 @@ $dblink = array();
  * Each call to the database increments this counter.
  *
  * @global integer $dbcalls
+ * @access private
  */
 global $dbcalls;
 $dbcalls = 0;
@@ -72,11 +79,12 @@ $dbcalls = 0;
  * resource. eg "read", "write", or "readwrite".
  *
  * @return void
+ * @throws DatabaseException
  * @access private
  */
 function establish_db_link($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[$dblinkname])) {
@@ -120,7 +128,8 @@ function establish_db_link($dblinkname = "readwrite") {
 
 	// Set up cache if global not initialized and query cache not turned off
 	if ((!$DB_QUERY_CACHE) && (!$db_cache_off)) {
-		$DB_QUERY_CACHE = new ElggStaticVariableCache('db_query_cache');
+		// @todo if we keep this cache in 1.9, expose the size as a config parameter
+		$DB_QUERY_CACHE = new ElggLRUCache(200);
 	}
 }
 
@@ -134,7 +143,7 @@ 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 +206,7 @@ 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 +225,7 @@ 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 $link  The database link resource to user.
  *
  * @return mixed An object of the query's result, or FALSE
@@ -240,14 +249,14 @@ function explain_query($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 ($query == NULL) {
 		throw new DatabaseException(elgg_echo('DatabaseException:InvalidQuery'));
@@ -275,7 +284,7 @@ function execute_query($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   $handler A callback function to pass the results array to
  *
  * @return true
@@ -386,20 +395,18 @@ function get_data_row($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.
-	// http://trac.elgg.org/ticket/4049
+	// https://github.com/elgg/elgg/issues/4049
 	$hash = (string)$callback . (int)$single . $query;
 
 	// Is cached?
 	if ($DB_QUERY_CACHE) {
-		$cached_query = $DB_QUERY_CACHE[$hash];
-
-		if ($cached_query !== FALSE) {
+		if (isset($DB_QUERY_CACHE[$hash])) {
 			elgg_log("DB query $query results returned from cache (hash: $hash)", 'NOTICE');
-			return $cached_query;
+			return $DB_QUERY_CACHE[$hash];
 		}
 	}
 
@@ -410,7 +417,7 @@ 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 ($is_callable) {
@@ -451,18 +458,12 @@ function elgg_query_runner($query, $callback = null, $single = false) {
  * @access private
  */
 function insert_data($query) {
-	global $CONFIG, $DB_QUERY_CACHE;
 
 	elgg_log("DB query $query", 'NOTICE');
 	
 	$dblink = get_db_link('write');
 
-	// Invalidate query cache
-	if ($DB_QUERY_CACHE) {
-		$DB_QUERY_CACHE->clear();
-	}
-
-	elgg_log("Query cache invalidated", 'NOTICE');
+	_elgg_invalidate_query_cache();
 
 	if (execute_query("$query", $dblink)) {
 		return mysql_insert_id($dblink);
@@ -472,7 +473,7 @@ function insert_data($query) {
 }
 
 /**
- * Update a row in the database.
+ * Update the database.
  *
  * @note Altering the DB invalidates all queries in {@link $DB_QUERY_CACHE}.
  *
@@ -482,17 +483,12 @@ function insert_data($query) {
  * @access private
  */
 function update_data($query) {
-	global $CONFIG, $DB_QUERY_CACHE;
 
 	elgg_log("DB query $query", 'NOTICE');
 
 	$dblink = get_db_link('write');
 
-	// Invalidate query cache
-	if ($DB_QUERY_CACHE) {
-		$DB_QUERY_CACHE->clear();
-		elgg_log("Query cache invalidated", 'NOTICE');
-	}
+	_elgg_invalidate_query_cache();
 
 	if (execute_query("$query", $dblink)) {
 		return TRUE;
@@ -502,7 +498,7 @@ function update_data($query) {
 }
 
 /**
- * Remove a row from the database.
+ * Remove data from the database.
  *
  * @note Altering the DB invalidates all queries in {@link $DB_QUERY_CACHE}.
  *
@@ -512,17 +508,12 @@ function update_data($query) {
  * @access private
  */
 function delete_data($query) {
-	global $CONFIG, $DB_QUERY_CACHE;
 
 	elgg_log("DB query $query", 'NOTICE');
 
 	$dblink = get_db_link('write');
 
-	// Invalidate query cache
-	if ($DB_QUERY_CACHE) {
-		$DB_QUERY_CACHE->clear();
-		elgg_log("Query cache invalidated", 'NOTICE');
-	}
+	_elgg_invalidate_query_cache();
 
 	if (execute_query("$query", $dblink)) {
 		return mysql_affected_rows($dblink);
@@ -531,6 +522,22 @@ function delete_data($query) {
 	return FALSE;
 }
 
+/**
+ * Invalidate the query cache
+ *
+ * @access private
+ */
+function _elgg_invalidate_query_cache() {
+	global $DB_QUERY_CACHE;
+	if ($DB_QUERY_CACHE instanceof ElggLRUCache) {
+		$DB_QUERY_CACHE->clear();
+		elgg_log("Query cache invalidated", 'NOTICE');
+	} elseif ($DB_QUERY_CACHE) {
+		// In case someone sets the cache to an array and primes it with data
+		$DB_QUERY_CACHE = array();
+		elgg_log("Query cache invalidated", 'NOTICE');
+	}
+}
 
 /**
  * Return tables matching the database prefix {@link $CONFIG->dbprefix}% in the currently
@@ -638,7 +645,7 @@ function run_sql_script($scriptlocation) {
 			$statement = str_replace("prefix_", $CONFIG->dbprefix, $statement);
 			if (!empty($statement)) {
 				try {
-					$result = update_data($statement);
+					update_data($statement);
 				} catch (DatabaseException $e) {
 					$errors[] = $e->getMessage();
 				}
@@ -661,7 +668,7 @@ function run_sql_script($scriptlocation) {
 
 /**
  * Format a query string for logging
- * 
+ *
  * @param string $query Query string
  * @return string
  * @access private
diff --git a/engine/lib/deprecated-1.7.php b/engine/lib/deprecated-1.7.php
index 519eea89d..ee95b5611 100644
--- a/engine/lib/deprecated-1.7.php
+++ b/engine/lib/deprecated-1.7.php
@@ -1137,6 +1137,7 @@ function make_register_object($register_name, $register_value, $children_array =
  * @param int $guid GUID
  *
  * @return 1
+ * @deprecated 1.7
  */
 function delete_object_entity($guid) {
 	system_message(elgg_echo('deprecatedfunction', array('delete_user_entity')));
@@ -1154,6 +1155,7 @@ function delete_object_entity($guid) {
  * @param int $guid User GUID
  *
  * @return 1
+ * @deprecated 1.7
  */
 function delete_user_entity($guid) {
 	system_message(elgg_echo('deprecatedfunction', array('delete_user_entity')));
diff --git a/engine/lib/deprecated-1.8.php b/engine/lib/deprecated-1.8.php
index 4b9d41543..91068d047 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' => $offset
 	));
@@ -3414,6 +3414,7 @@ function list_annotations($entity_guid, $name = "", $limit = 25, $asc = true) {
  * @param unknown_type $timeupper
  * @param unknown_type $calculation
  * @internal Don't use this at all.
+ * @deprecated 1.8 Use elgg_get_annotations()
  */
 function elgg_deprecated_annotation_calculation($entity_guid = 0, $entity_type = "", $entity_subtype = "",
 $name = "", $value = "", $value_type = "", $owner_guid = 0, $timelower = 0,
@@ -4667,6 +4668,7 @@ function display_widget(ElggObject $widget) {
  *
  * @param ElggEntity $entity
  * @return int Number of comments
+ * @deprecated 1.8 Use ElggEntity->countComments()
  */
 function elgg_count_comments($entity) {
 	elgg_deprecated_notice('elgg_count_comments() is deprecated by ElggEntity->countComments()', 1.8);
@@ -4772,3 +4774,47 @@ function default_page_handler($page, $handler) {
 
 	return FALSE;
 }
+
+/**
+ * Invalidate this class's entry in the cache.
+ *
+ * @param int $guid The entity guid
+ *
+ * @return void
+ * @access private
+ * @deprecated 1.8
+ */
+function invalidate_cache_for_entity($guid) {
+	elgg_deprecated_notice('invalidate_cache_for_entity() is a private function and should not be used.', 1.8);
+	_elgg_invalidate_cache_for_entity($guid);
+}
+
+/**
+ * Cache an entity.
+ *
+ * Stores an entity in $ENTITY_CACHE;
+ *
+ * @param ElggEntity $entity Entity to cache
+ *
+ * @return void
+ * @access private
+ * @deprecated 1.8
+ */
+function cache_entity(ElggEntity $entity) {
+	elgg_deprecated_notice('cache_entity() is a private function and should not be used.', 1.8);
+	_elgg_cache_entity($entity);
+}
+
+/**
+ * Retrieve a entity from the cache.
+ *
+ * @param int $guid The guid
+ *
+ * @return ElggEntity|bool false if entity not cached, or not fully loaded
+ * @access private
+ * @deprecated 1.8
+ */
+function retrieve_cached_entity($guid) {
+	elgg_deprecated_notice('retrieve_cached_entity() is a private function and should not be used.', 1.8);
+	return _elgg_retrieve_cached_entity($guid);
+}
diff --git a/engine/lib/elgglib.php b/engine/lib/elgglib.php
index 540605876..34111c69d 100644
--- a/engine/lib/elgglib.php
+++ b/engine/lib/elgglib.php
@@ -93,10 +93,17 @@ function elgg_register_library($name, $location) {
  * @return void
  * @throws InvalidParameterException
  * @since 1.8.0
+ * @todo return boolean in 1.9 to indicate whether the library has been loaded
  */
 function elgg_load_library($name) {
 	global $CONFIG;
 
+	static $loaded_libraries = array();
+
+	if (in_array($name, $loaded_libraries)) {
+		return;
+	}
+
 	if (!isset($CONFIG->libraries)) {
 		$CONFIG->libraries = array();
 	}
@@ -113,6 +120,8 @@ function elgg_load_library($name) {
 		);
 		throw new InvalidParameterException($error);
 	}
+
+	$loaded_libraries[] = $name;
 }
 
 /**
@@ -124,12 +133,11 @@ 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 $CONFIG;
-
-	if (!headers_sent()) {
+	if (!headers_sent($file, $line)) {
 		if ($location === REFERER) {
 			$location = $_SERVER['HTTP_REFERER'];
 		}
@@ -148,7 +156,7 @@ function forward($location = "", $reason = 'system') {
 			exit;
 		}
 	} else {
-		throw new SecurityException(elgg_echo('SecurityException:ForwardFailedToRedirect'));
+		throw new SecurityException(elgg_echo('SecurityException:ForwardFailedToRedirect', array($file, $line)));
 	}
 }
 
@@ -384,7 +392,7 @@ 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] = $item;
 	}
 }
@@ -528,7 +536,7 @@ function sanitise_filepath($path, $append_slash = TRUE) {
  * @param string $register Types of message: "error", "success" (default: success)
  * @param bool   $count    Count the number of messages (default: false)
  *
- * @return true|false|array Either the array of messages, or a response regarding
+ * @return bool|array Either the array of messages, or a response regarding
  *                          whether the message addition was successful.
  * @todo Clean up. Separate registering messages and retrieving them.
  */
@@ -562,7 +570,7 @@ function system_messages($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 $count;
@@ -738,7 +746,7 @@ function elgg_unregister_event_handler($event, $object_type, $callback) {
  * @tip When referring to events, the preferred syntax is "event, type".
  *
  * @internal Only rarely should events be changed, added, or removed in core.
- * When making changes to events, be sure to first create a ticket in trac.
+ * When making changes to events, be sure to first create a ticket on Github.
  *
  * @internal @tip Think of $object_type as the primary namespace element, and
  * $event as the secondary namespace.
@@ -839,7 +847,7 @@ function elgg_trigger_event($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      $priority The priority - 500 is default, lower numbers called first
  *
  * @return bool
@@ -885,7 +893,7 @@ function elgg_register_plugin_hook_handler($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 $callback    The PHP callback to be removed
  *
  * @return void
  * @since 1.8.0
@@ -1060,6 +1068,7 @@ function _elgg_php_exception_handler($exception) {
  * @param array  $vars     An array that points to the active symbol table where error occurred
  *
  * @return true
+ * @throws Exception
  * @access private
  * @todo Replace error_log calls with elgg_log calls.
  */
@@ -1185,6 +1194,11 @@ function elgg_dump($value, $to_screen = TRUE, $level = 'NOTICE') {
 		$to_screen = FALSE;
 	}
 
+	// Do not want to write to JS or CSS pages
+	if (elgg_in_context('js') || elgg_in_context('css')) {
+		$to_screen = FALSE;
+	}
+
 	if ($to_screen == TRUE) {
 		echo '<pre>';
 		print_r($value);
@@ -1292,8 +1306,6 @@ function elgg_deprecated_notice($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'] . "://";
@@ -1338,7 +1350,7 @@ function full_url() {
 		"" : (":" . $_SERVER["SERVER_PORT"]);
 
 	// This is here to prevent XSS in poorly written browsers used by 80% of the population.
-	// {@trac [5813]}
+	// https://github.com/Elgg/Elgg/commit/0c947e80f512cb0a482b1864fd0a6965c8a0cd4a
 	$quotes = array('\'', '"');
 	$encoded = array('%27', '%22');
 
@@ -1354,7 +1366,7 @@ 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 +1397,10 @@ 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 bool $html_encode HTML encode the url? (default: false)
+ * @param string $url         Full action URL
+ * @param bool   $html_encode HTML encode the url? (default: false)
  *
- * @return str URL with action tokens
+ * @return string URL with action tokens
  * @since 1.7.0
  * @link http://docs.elgg.org/Tutorials/Actions
  */
@@ -1440,17 +1452,17 @@ function elgg_http_remove_url_query_element($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 array $elements Key/value pairs to add to 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 $elements) {
@@ -1487,8 +1499,6 @@ function elgg_http_add_url_query_elements($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 +1637,7 @@ $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 +1656,7 @@ $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 +1672,7 @@ 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 $setting The php.ini setting
  *
  * @return int
  * @since 1.7.0
@@ -1677,8 +1687,10 @@ function elgg_get_ini_setting_in_bytes($setting) {
 	switch($last) {
 		case 'g':
 			$val *= 1024;
+			// fallthrough intentional
 		case 'm':
 			$val *= 1024;
+			// fallthrough intentional
 		case 'k':
 			$val *= 1024;
 	}
@@ -1835,7 +1847,7 @@ function elgg_ajax_page_handler($page) {
  *
  * @param array $page The page array
  *
- * @return void
+ * @return bool
  * @elgg_pagehandler css
  * @access private
  */
@@ -1899,6 +1911,7 @@ function elgg_cacheable_view_page_handler($page, $type) {
 		echo $return;
 		return true;
 	}
+	return false;
 }
 
 /**
@@ -2220,7 +2233,7 @@ 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, $params) {
@@ -2232,7 +2245,10 @@ function elgg_api_test($hook, $type, $value, $params) {
 }
 
 /**#@+
- * Controlls access levels on ElggEntity entities, metadata, and annotations.
+ * Controls access levels on ElggEntity entities, metadata, and annotations.
+ *
+ * @warning ACCESS_DEFAULT is a place holder for the input/access view. Do not
+ * use it when saving an entity.
  *
  * @var int
  */
@@ -2266,7 +2282,7 @@ 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..4fcf1c657 100644
--- a/engine/lib/entities.php
+++ b/engine/lib/entities.php
@@ -17,6 +17,15 @@ global $ENTITY_CACHE;
 $ENTITY_CACHE = array();
 
 /**
+ * GUIDs of entities banned from the entity cache (during this request)
+ *
+ * @global array $ENTITY_CACHE_DISABLED_GUIDS
+ * @access private
+ */
+global $ENTITY_CACHE_DISABLED_GUIDS;
+$ENTITY_CACHE_DISABLED_GUIDS = array();
+
+/**
  * Cache subtypes and related class names.
  *
  * @global array|null $SUBTYPE_CACHE array once populated from DB, initially null
@@ -26,14 +35,42 @@ global $SUBTYPE_CACHE;
 $SUBTYPE_CACHE = null;
 
 /**
+ * Remove this entity from the entity cache and make sure it is not re-added
+ *
+ * @param int $guid The entity guid
+ *
+ * @access private
+ * @todo this is a workaround until #5604 can be implemented
+ */
+function _elgg_disable_caching_for_entity($guid) {
+	global $ENTITY_CACHE_DISABLED_GUIDS;
+
+	_elgg_invalidate_cache_for_entity($guid);
+	$ENTITY_CACHE_DISABLED_GUIDS[$guid] = true;
+}
+
+/**
+ * Allow this entity to be stored in the entity cache
+ *
+ * @param int $guid The entity guid
+ *
+ * @access private
+ */
+function _elgg_enable_caching_for_entity($guid) {
+	global $ENTITY_CACHE_DISABLED_GUIDS;
+
+	unset($ENTITY_CACHE_DISABLED_GUIDS[$guid]);
+}
+
+/**
  * Invalidate this class's entry in the cache.
  *
  * @param int $guid The entity guid
  *
- * @return null
+ * @return void
  * @access private
  */
-function invalidate_cache_for_entity($guid) {
+function _elgg_invalidate_cache_for_entity($guid) {
 	global $ENTITY_CACHE;
 
 	$guid = (int)$guid;
@@ -50,14 +87,14 @@ function invalidate_cache_for_entity($guid) {
  *
  * @param ElggEntity $entity Entity to cache
  *
- * @return null
- * @see retrieve_cached_entity()
- * @see invalidate_cache_for_entity()
+ * @return void
+ * @see _elgg_retrieve_cached_entity()
+ * @see _elgg_invalidate_cache_for_entity()
  * @access private
- * TODO(evan): Use an ElggCache object
+ * @todo Use an ElggCache object
  */
-function cache_entity(ElggEntity $entity) {
-	global $ENTITY_CACHE;
+function _elgg_cache_entity(ElggEntity $entity) {
+	global $ENTITY_CACHE, $ENTITY_CACHE_DISABLED_GUIDS;
 
 	// Don't cache non-plugin entities while access control is off, otherwise they could be
 	// exposed to users who shouldn't see them when control is re-enabled.
@@ -65,8 +102,13 @@ function cache_entity(ElggEntity $entity) {
 		return;
 	}
 
+	$guid = $entity->getGUID();
+	if (isset($ENTITY_CACHE_DISABLED_GUIDS[$guid])) {
+		return;
+	}
+
 	// Don't store too many or we'll have memory problems
-	// TODO(evan): Pick a less arbitrary limit
+	// @todo Pick a less arbitrary limit
 	if (count($ENTITY_CACHE) > 256) {
 		$random_guid = array_rand($ENTITY_CACHE);
 
@@ -79,7 +121,7 @@ function cache_entity(ElggEntity $entity) {
 		elgg_get_metadata_cache()->clear($random_guid);
 	}
 
-	$ENTITY_CACHE[$entity->guid] = $entity;
+	$ENTITY_CACHE[$guid] = $entity;
 }
 
 /**
@@ -88,11 +130,11 @@ function cache_entity(ElggEntity $entity) {
  * @param int $guid The guid
  *
  * @return ElggEntity|bool false if entity not cached, or not fully loaded
- * @see cache_entity()
- * @see invalidate_cache_for_entity()
+ * @see _elgg_cache_entity()
+ * @see _elgg_invalidate_cache_for_entity()
  * @access private
  */
-function retrieve_cached_entity($guid) {
+function _elgg_retrieve_cached_entity($guid) {
 	global $ENTITY_CACHE;
 
 	if (isset($ENTITY_CACHE[$guid])) {
@@ -105,31 +147,6 @@ function retrieve_cached_entity($guid) {
 }
 
 /**
- * As retrieve_cached_entity, but returns the result as a stdClass
- * (compatible with load functions that expect a database row.)
- *
- * @param int $guid The guid
- *
- * @return mixed
- * @todo unused
- * @access private
- */
-function retrieve_cached_entity_row($guid) {
-	$obj = retrieve_cached_entity($guid);
-	if ($obj) {
-		$tmp = new stdClass;
-
-		foreach ($obj as $k => $v) {
-			$tmp->$k = $v;
-		}
-
-		return $tmp;
-	}
-
-	return false;
-}
-
-/**
  * Return the id for a given subtype.
  *
  * ElggEntity objects have a type and a subtype.  Subtypes
@@ -432,7 +449,7 @@ function update_subtype($type, $subtype, $class = '') {
  * @param int $time_created   The time creation timestamp
  *
  * @return bool
- * @link http://docs.elgg.org/DataModel/Entities
+ * @throws InvalidParameterException
  * @access private
  */
 function update_entity($guid, $owner_guid, $access_id, $container_guid = null, $time_created = null) {
@@ -455,6 +472,10 @@ function update_entity($guid, $owner_guid, $access_id, $container_guid = null, $
 		$time_created = (int) $time_created;
 	}
 
+	if ($access_id == ACCESS_DEFAULT) {
+		throw new InvalidParameterException('ACCESS_DEFAULT is not a valid access level. See its documentation in elgglib.h');
+	}
+
 	if ($entity && $entity->canEdit()) {
 		if (elgg_trigger_event('update', $entity->type, $entity)) {
 			$ret = update_data("UPDATE {$CONFIG->dbprefix}entities
@@ -531,6 +552,7 @@ 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;
 			}
@@ -580,7 +602,6 @@ $container_guid = 0) {
 	$type = sanitise_string($type);
 	$subtype_id = add_subtype($type, $subtype);
 	$owner_guid = (int)$owner_guid;
-	$access_id = (int)$access_id;
 	$time = time();
 	if ($site_guid == 0) {
 		$site_guid = $CONFIG->site_guid;
@@ -589,6 +610,10 @@ $container_guid = 0) {
 	if ($container_guid == 0) {
 		$container_guid = $owner_guid;
 	}
+	$access_id = (int)$access_id;
+	if ($access_id == ACCESS_DEFAULT) {
+		throw new InvalidParameterException('ACCESS_DEFAULT is not a valid access level. See its documentation in elgglib.h');
+	}
 
 	$user_guid = elgg_get_logged_in_user_guid();
 	if (!can_write_to_container($user_guid, $owner_guid, $type, $subtype)) {
@@ -736,7 +761,7 @@ function get_entity($guid) {
 	// @todo We need a single Memcache instance with a shared pool of namespace wrappers. This function would pull an instance from the pool.
 	static $shared_cache;
 
-	// We could also use: if (!(int) $guid) { return FALSE }, 
+	// We could also use: if (!(int) $guid) { return FALSE },
 	// but that evaluates to a false positive for $guid = TRUE.
 	// This is a bit slower, but more thorough.
 	if (!is_numeric($guid) || $guid === 0 || $guid === '0') {
@@ -744,7 +769,7 @@ function get_entity($guid) {
 	}
 	
 	// Check local cache first
-	$new_entity = retrieve_cached_entity($guid);
+	$new_entity = _elgg_retrieve_cached_entity($guid);
 	if ($new_entity) {
 		return $new_entity;
 	}
@@ -766,7 +791,7 @@ function get_entity($guid) {
 
 	if ($shared_cache) {
 		$cached_entity = $shared_cache->load($guid);
-		// @todo store ACLs in memcache http://trac.elgg.org/ticket/3018#comment:3
+		// @todo store ACLs in memcache https://github.com/elgg/elgg/issues/3018#issuecomment-13662617
 		if ($cached_entity) {
 			// @todo use ACL and cached entity access_id to determine if user can see it
 			return $cached_entity;
@@ -781,7 +806,7 @@ function get_entity($guid) {
 	}
 
 	if ($new_entity) {
-		cache_entity($new_entity);
+		_elgg_cache_entity($new_entity);
 	}
 	return $new_entity;
 }
@@ -908,6 +933,8 @@ function elgg_get_entities(array $options = array()) {
 		'joins'					=>	array(),
 
 		'callback'				=> 'entity_row_to_elggstar',
+
+		'__ElggBatch'			=> null,
 	);
 
 	$options = array_merge($defaults, $options);
@@ -1025,7 +1052,7 @@ function elgg_get_entities(array $options = array()) {
 		}
 
 		if ($options['callback'] === 'entity_row_to_elggstar') {
-			$dt = _elgg_fetch_entities_from_sql($query);
+			$dt = _elgg_fetch_entities_from_sql($query, $options['__ElggBatch']);
 		} else {
 			$dt = get_data($query, $options['callback']);
 		}
@@ -1036,7 +1063,7 @@ function elgg_get_entities(array $options = array()) {
 			foreach ($dt as $item) {
 				// A custom callback could result in items that aren't ElggEntity's, so check for them
 				if ($item instanceof ElggEntity) {
-					cache_entity($item);
+					_elgg_cache_entity($item);
 					// plugins usually have only settings
 					if (!$item instanceof ElggPlugin) {
 						$guids[] = $item->guid;
@@ -1060,13 +1087,14 @@ function elgg_get_entities(array $options = array()) {
 /**
  * Return entities from an SQL query generated by elgg_get_entities.
  *
- * @param string $sql
+ * @param string    $sql
+ * @param ElggBatch $batch
  * @return ElggEntity[]
  *
  * @access private
  * @throws LogicException
  */
-function _elgg_fetch_entities_from_sql($sql) {
+function _elgg_fetch_entities_from_sql($sql, ElggBatch $batch = null) {
 	static $plugin_subtype;
 	if (null === $plugin_subtype) {
 		$plugin_subtype = get_subtype_id('object', 'plugin');
@@ -1101,7 +1129,7 @@ function _elgg_fetch_entities_from_sql($sql) {
 		if (empty($row->guid) || empty($row->type)) {
 			throw new LogicException('Entity row missing guid or type');
 		}
-		if ($entity = retrieve_cached_entity($row->guid)) {
+		if ($entity = _elgg_retrieve_cached_entity($row->guid)) {
 			$rows[$i] = $entity;
 			continue;
 		}
@@ -1119,16 +1147,17 @@ function _elgg_fetch_entities_from_sql($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)$secondary_row);
+				}
 			}
 		}
 	}
@@ -1142,6 +1171,11 @@ function _elgg_fetch_entities_from_sql($sql) {
 			} catch (IncompleteEntityException $e) {
 				// don't let incomplete entities throw fatal errors
 				unset($rows[$i]);
+
+				// report incompletes to the batch process that spawned this query
+				if ($batch) {
+					$batch->reportIncompleteEntity($row);
+				}
 			}
 		}
 	}
@@ -1217,13 +1251,24 @@ 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;
+						}
 					}
 				}
 
@@ -1428,8 +1473,10 @@ function elgg_list_entities(array $options = array(), $getter = 'elgg_get_entiti
 	global $autofeed;
 	$autofeed = true;
 
+	$offset_key = isset($options['offset_key']) ? $options['offset_key'] : 'offset';
+
 	$defaults = array(
-		'offset' => (int) max(get_input('offset', 0), 0),
+		'offset' => (int) max(get_input($offset_key, 0), 0),
 		'limit' => (int) max(get_input('limit', 10), 0),
 		'full_view' => TRUE,
 		'list_type_toggle' => FALSE,
@@ -1459,11 +1506,13 @@ 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 $order_by       Order_by SQL order by clause
  *
@@ -1613,7 +1662,7 @@ function disable_entity($guid, $reason = "", $recursive = true) {
 
 				$entity->disableMetadata();
 				$entity->disableAnnotations();
-				invalidate_cache_for_entity($guid);
+				_elgg_invalidate_cache_for_entity($guid);
 
 				$res = update_data("UPDATE {$CONFIG->dbprefix}entities
 					SET enabled = 'no'
@@ -1629,8 +1678,8 @@ function disable_entity($guid, $reason = "", $recursive = true) {
 /**
  * Enable an entity.
  *
- * @warning In order to enable an entity using ElggEntity::enable(),
- * you must first use {@link access_show_hidden_entities()}.
+ * @warning In order to enable an entity, you must first use
+ * {@link access_show_hidden_entities()}.
  *
  * @param int  $guid      GUID of entity to enable
  * @param bool $recursive Recursively enable all entities disabled with the entity?
@@ -1711,7 +1760,7 @@ function delete_entity($guid, $recursive = true) {
 
 				// delete cache
 				if (isset($ENTITY_CACHE[$guid])) {
-					invalidate_cache_for_entity($guid);
+					_elgg_invalidate_cache_for_entity($guid);
 				}
 				
 				// If memcache is available then delete this entry from the cache
@@ -1758,6 +1807,10 @@ function delete_entity($guid, $recursive = true) {
 					elgg_set_ignore_access($ia);
 				}
 
+				$entity_disable_override = access_get_show_hidden_status();
+				access_show_hidden_entities(true);
+				$ia = elgg_set_ignore_access(true);
+
 				// Now delete the entity itself
 				$entity->deleteMetadata();
 				$entity->deleteOwnedMetadata();
@@ -1765,6 +1818,9 @@ function delete_entity($guid, $recursive = true) {
 				$entity->deleteOwnedAnnotations();
 				$entity->deleteRelationships();
 
+				access_show_hidden_entities($entity_disable_override);
+				elgg_set_ignore_access($ia);
+
 				elgg_delete_river(array('subject_guid' => $guid));
 				elgg_delete_river(array('object_guid' => $guid));
 				remove_all_private_settings($guid);
@@ -2072,7 +2128,7 @@ function can_edit_entity_metadata($entity_guid, $user_guid = 0, $metadata = null
 
 		$return = null;
 
-		if ($metadata->owner_guid == 0) {
+		if ($metadata && ($metadata->owner_guid == 0)) {
 			$return = true;
 		}
 		if (is_null($return)) {
@@ -2413,6 +2469,7 @@ function elgg_instanceof($entity, $type = NULL, $subtype = NULL, $class = NULL)
 	$return = ($entity instanceof ElggEntity);
 
 	if ($type) {
+		/* @var ElggEntity $entity */
 		$return = $return && ($entity->getType() == $type);
 	}
 
@@ -2472,11 +2529,18 @@ function update_entity_last_action($guid, $posted = NULL) {
 function entities_gc() {
 	global $CONFIG;
 
-	$tables = array ('sites_entity', 'objects_entity', 'groups_entity', 'users_entity');
+	$tables = array(
+		'site' => 'sites_entity',
+		'object' => 'objects_entity',
+		'group' => 'groups_entity',
+		'user' => 'users_entity'
+	);
 
-	foreach ($tables as $table) {
-		delete_data("DELETE from {$CONFIG->dbprefix}{$table}
-			where guid NOT IN (SELECT guid from {$CONFIG->dbprefix}entities)");
+	foreach ($tables as $type => $table) {
+		delete_data("DELETE FROM {$CONFIG->dbprefix}{$table}
+			WHERE guid NOT IN (SELECT guid FROM {$CONFIG->dbprefix}entities)");
+		delete_data("DELETE FROM {$CONFIG->dbprefix}entities
+			WHERE type = '$type' AND guid NOT IN (SELECT guid FROM {$CONFIG->dbprefix}{$table})");
 	}
 }
 
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..8323bd3ce 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);
@@ -124,14 +126,20 @@ function import_extender_plugin_hook($hook, $entity_type, $returnvalue, $params)
  * @return bool
  */
 function can_edit_extender($extender_id, $type, $user_guid = 0) {
-	if (!elgg_is_logged_in()) {
-		return false;
+	// @todo Since Elgg 1.0, Elgg has returned false from can_edit_extender()
+	// if no user was logged in. This breaks the access override. This is a
+	// temporary work around. This function needs to be rewritten in Elgg 1.9 
+	if (!elgg_check_access_overrides($user_guid)) {
+		if (!elgg_is_logged_in()) {
+			return false;
+		}
 	}
 
 	$user_guid = (int)$user_guid;
-	$user = get_entity($user_guid);
+	$user = get_user($user_guid);
 	if (!$user) {
 		$user = elgg_get_logged_in_user_entity();
+		$user_guid = elgg_get_logged_in_user_guid();
 	}
 
 	$functionname = "elgg_get_{$type}_from_id";
@@ -147,16 +155,16 @@ function can_edit_extender($extender_id, $type, $user_guid = 0) {
 	/* @var ElggExtender $extender */
 
 	// If the owner is the specified user, great! They can edit.
-	if ($extender->getOwnerGUID() == $user->getGUID()) {
+	if ($extender->getOwnerGUID() == $user_guid) {
 		return true;
 	}
 
 	// If the user can edit the entity this is attached to, great! They can edit.
-	if (can_edit_entity($extender->entity_guid, $user->getGUID())) {
+	if (can_edit_entity($extender->entity_guid, $user_guid)) {
 		return true;
 	}
 
-	// Trigger plugin hooks
+	// Trigger plugin hook - note that $user may be null
 	$params = array('entity' => $extender->getEntity(), 'user' => $user);
 	return elgg_trigger_plugin_hook('permissions_check', $type, $params, false);
 }
diff --git a/engine/lib/filestore.php b/engine/lib/filestore.php
index 93a127257..a3c7ba439 100644
--- a/engine/lib/filestore.php
+++ b/engine/lib/filestore.php
@@ -308,8 +308,6 @@ function get_image_resize_parameters($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  $params Params
diff --git a/engine/lib/group.php b/engine/lib/group.php
index 5a38e1ea6..6ded8a825 100644
--- a/engine/lib/group.php
+++ b/engine/lib/group.php
@@ -170,7 +170,7 @@ function get_group_members($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' => $count,
@@ -240,9 +240,11 @@ function leave_group($group_guid, $user_guid) {
  */
 function get_users_membership($user_guid) {
 	$options = array(
+		'type' => 'group',
 		'relationship' => 'member',
 		'relationship_guid' => $user_guid,
-		'inverse_relationship' => FALSE
+		'inverse_relationship' => false,
+		'limit' => false,
 	);
 	return elgg_get_entities_from_relationship($options);
 }
diff --git a/engine/lib/input.php b/engine/lib/input.php
index 6d1646e1a..80b0b8766 100644
--- a/engine/lib/input.php
+++ b/engine/lib/input.php
@@ -60,8 +60,8 @@ function get_input($variable, $default = NULL, $filter_result = TRUE) {
  *
  * Note: this function does not handle nested arrays (ex: form input of param[m][n])
  *
- * @param string $variable The name of the variable
- * @param string $value    The value of the variable
+ * @param string          $variable The name of the variable
+ * @param string|string[] $value    The value of the variable
  *
  * @return void
  */
@@ -226,6 +226,8 @@ function elgg_clear_sticky_value($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..61ba91ddb 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) {
@@ -141,6 +139,9 @@ function get_language() {
 	return false;
 }
 
+/**
+ * @access private
+ */
 function _elgg_load_translations() {
 	global $CONFIG;
 
@@ -148,7 +149,7 @@ 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 +178,7 @@ 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 $CONFIG;
@@ -229,23 +230,37 @@ function register_translations($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);
+		}
 	}
 
 	$LANG_RELOAD_ALL_RUN = true;
@@ -337,14 +352,3 @@ function get_missing_language_keys($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..1534c7d7b 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";
@@ -139,7 +139,7 @@ function elgg_get_entities_from_location(array $options = array()) {
 /**
  * Returns a viewable list of entities from location
  *
- * @param array $options
+ * @param array $options Options array
  *
  * @see elgg_list_entities()
  * @see elgg_get_entities_from_location()
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/memcache.php b/engine/lib/memcache.php
index f79fba4a9..79b87e850 100644
--- a/engine/lib/memcache.php
+++ b/engine/lib/memcache.php
@@ -35,3 +35,23 @@ function is_memcache_available() {
 
 	return $memcache_available;
 }
+
+/**
+ * Invalidate an entity in memcache
+ *
+ * @param int $entity_guid The GUID of the entity to invalidate
+ *
+ * @return void
+ * @access private
+ */
+function _elgg_invalidate_memcache_for_entity($entity_guid) {
+	static $newentity_cache;
+	

+	if ((!$newentity_cache) && (is_memcache_available())) {

+		$newentity_cache = new ElggMemcache('new_entity_cache');

+	}
+	

+	if ($newentity_cache) {

+		$newentity_cache->delete($entity_guid);

+	}
+}
\ No newline at end of file
diff --git a/engine/lib/metadata.php b/engine/lib/metadata.php
index f76c20f24..fdb1b85f6 100644
--- a/engine/lib/metadata.php
+++ b/engine/lib/metadata.php
@@ -191,19 +191,19 @@ function update_metadata($id, $name, $value, $value_type, $owner_guid, $access_i
 	}
 
 	// Add the metastring
-	$value = add_metastring($value);
-	if (!$value) {
+	$value_id = add_metastring($value);
+	if (!$value_id) {
 		return false;
 	}
 
-	$name = add_metastring($name);
-	if (!$name) {
+	$name_id = add_metastring($name);
+	if (!$name_id) {
 		return false;
 	}
 
 	// If ok then add it
 	$query = "UPDATE {$CONFIG->dbprefix}metadata"
-		. " set name_id='$name', value_id='$value', value_type='$value_type', access_id=$access_id,"
+		. " set name_id='$name_id', value_id='$value_id', value_type='$value_type', access_id=$access_id,"
 		. " owner_guid=$owner_guid where id=$id";
 
 	$result = update_data($query);
@@ -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);
 }
@@ -292,21 +300,22 @@ function elgg_get_metadata(array $options = array()) {
  *          This requires at least one constraint: metadata_owner_guid(s),
  *          metadata_name(s), metadata_value(s), or guid(s) must be set.
  *
- * @warning This returns null on no ops.
- *
  * @param array $options An options array. {@see elgg_get_metadata()}
- * @return mixed Null if the metadata name is invalid. Bool on success or fail.
+ * @return bool|null true on success, false on failure, null if no metadata to delete.
  * @since 1.8.0
  */
 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;
 }
 
 /**
@@ -314,10 +323,8 @@ function elgg_delete_metadata(array $options) {
  *
  * @warning Unlike elgg_get_metadata() this will not accept an empty options array!
  *
- * @warning This returns null on no ops.
- *
  * @param array $options An options array. {@See elgg_get_metadata()}
- * @return mixed
+ * @return bool|null true on success, false on failure, null if no metadata disabled.
  * @since 1.8.0
  */
 function elgg_disable_metadata(array $options) {
@@ -326,9 +333,13 @@ function elgg_disable_metadata(array $options) {
 	}
 
 	elgg_get_metadata_cache()->invalidateByOptions('disable', $options);
+	
+	// if we can see hidden (disabled) we need to use the offset
+	// otherwise we risk an infinite loop if there are more than 50
+	$inc_offset = access_get_show_hidden_status();
 
 	$options['metastring_type'] = 'metadata';
-	return elgg_batch_metastring_based_objects($options, 'elgg_batch_disable_callback', false);
+	return elgg_batch_metastring_based_objects($options, 'elgg_batch_disable_callback', $inc_offset);
 }
 
 /**
@@ -336,10 +347,11 @@ function elgg_disable_metadata(array $options) {
  *
  * @warning Unlike elgg_get_metadata() this will not accept an empty options array!
  *
- * @warning This returns null on no ops.
+ * @warning In order to enable metadata, you must first use
+ * {@link access_show_hidden_entities()}.
  *
  * @param array $options An options array. {@See elgg_get_metadata()}
- * @return mixed
+ * @return bool|null true on success, false on failure, null if no metadata enabled.
  * @since 1.8.0
  */
 function elgg_enable_metadata(array $options) {
@@ -394,9 +406,11 @@ function elgg_enable_metadata(array $options) {
  *                                         'operand' => '=',
  *                                         'case_sensitive' => TRUE
  *                                        )
- * 	                             Currently if multiple values are sent via
+ *                               Currently if multiple values are sent via
  *                               an array (value => array('value1', 'value2')
  *                               the pair's operand will be forced to "IN".
+ *                               If passing "IN" as the operand and a string as the value, 
+ *                               the value must be a properly quoted and escaped string.
  *
  * 	metadata_name_value_pairs_operator => NULL|STR The operator to use for combining
  *                                        (name = value) OPERATOR (name = value); default AND
@@ -412,7 +426,7 @@ 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 +475,7 @@ 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
  */
@@ -608,6 +622,8 @@ $owner_guids = NULL) {
 			// if the operand is IN don't quote it because quoting should be done already.
 			if (is_numeric($pair['value'])) {
 				$value = sanitise_string($pair['value']);
+			} else if (is_bool($pair['value'])) {
+				$value = (int) $pair['value'];
 			} else if (is_array($pair['value'])) {
 				$values_array = array();
 
@@ -774,10 +790,10 @@ 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;
-
 }
 
 /**
@@ -909,8 +925,8 @@ function elgg_get_metadata_cache() {
  * Invalidate the metadata cache based on options passed to various *_metadata functions
  *
  * @param string $action  Action performed on metadata. "delete", "disable", or "enable"
- *
- * @param array $options  Options passed to elgg_(delete|disable|enable)_metadata
+ * @param array  $options Options passed to elgg_(delete|disable|enable)_metadata
+ * @return void
  */
 function elgg_invalidate_metadata_cache($action, array $options) {
 	// remove as little as possible, optimizing for common cases
diff --git a/engine/lib/metastrings.php b/engine/lib/metastrings.php
index cf6dd4d98..57d876c06 100644
--- a/engine/lib/metastrings.php
+++ b/engine/lib/metastrings.php
@@ -67,7 +67,7 @@ function get_metastring_id($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']) {
-		$options['metastring_calculation'] = 'count';
-	}
-
 	// For performance reasons we don't want the joins required for metadata / annotations
 	// unless we're going through one of their callbacks.
 	// this means we expect the functions passing different callbacks to pass their required joins.
@@ -426,9 +421,11 @@ function elgg_get_metastring_based_objects($options) {
 	if ($metastring_clauses) {
 		$wheres = array_merge($wheres, $metastring_clauses['wheres']);
 		$joins = array_merge($joins, $metastring_clauses['joins']);
+	} else {
+		$wheres[] = get_access_sql_suffix('n_table');
 	}
 
-	if ($options['metastring_calculation'] === ELGG_ENTITIES_NO_VALUE) {
+	if ($options['metastring_calculation'] === ELGG_ENTITIES_NO_VALUE && !$options['count']) {
 		$selects = array_unique($selects);
 		// evalutate selects
 		$select_str = '';
@@ -439,6 +436,9 @@ function elgg_get_metastring_based_objects($options) {
 		}
 
 		$query = "SELECT DISTINCT n_table.*{$select_str} FROM {$db_prefix}$type n_table";
+	} elseif ($options['count']) {
+		// count is over the entities
+		$query = "SELECT count(DISTINCT e.guid) as calculation FROM {$db_prefix}$type n_table";
 	} else {
 		$query = "SELECT {$options['metastring_calculation']}(v.string) as calculation FROM {$db_prefix}$type n_table";
 	}
@@ -467,7 +467,7 @@ function elgg_get_metastring_based_objects($options) {
 			$defaults['order_by']);
 	}
 
-	if ($options['metastring_calculation'] === ELGG_ENTITIES_NO_VALUE) {
+	if ($options['metastring_calculation'] === ELGG_ENTITIES_NO_VALUE && !$options['count']) {
 		if (isset($options['group_by'])) {
 			$options['group_by'] = sanitise_string($options['group_by']);
 			$query .= " GROUP BY {$options['group_by']}";
@@ -515,21 +515,16 @@ function elgg_get_metastring_sql($table, $names = null, $values = null,
 		&& !$ids
 		&& (!$pairs && $pairs !== 0)) {
 
-		return '';
+		return array();
 	}
 
 	$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.
 	$binary = ($case_sensitive) ? ' BINARY ' : '';
 
-	$access = get_access_sql_suffix($table);
-
 	$return = array (
 		'joins' => array (),
 		'wheres' => array()
@@ -594,13 +589,15 @@ function elgg_get_metastring_sql($table, $names = null, $values = null,
 	}
 
 	if ($names_where && $values_where) {
-		$wheres[] = "($names_where AND $values_where AND $access)";
+		$wheres[] = "($names_where AND $values_where)";
 	} elseif ($names_where) {
-		$wheres[] = "($names_where AND $access)";
+		$wheres[] = $names_where;
 	} elseif ($values_where) {
-		$wheres[] = "($values_where AND $access)";
+		$wheres[] = $values_where;
 	}
 
+	$wheres[] = get_access_sql_suffix($table);
+
 	if ($where = implode(' AND ', $wheres)) {
 		$return['wheres'][] = "($where)";
 	}
@@ -663,9 +660,10 @@ 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 +738,7 @@ function elgg_batch_metastring_based_objects(array $options, $callback, $inc_off
  *
  * @param int    $id   The metastring-based object's ID
  * @param string $type The type: annotation or metadata
- * @return mixed
+ * @return ElggMetadata|ElggAnnotation
  *
  * @since 1.8.0
  * @access private
@@ -806,6 +804,7 @@ function elgg_delete_metastring_based_object_by_id($id, $type) {
 			}
 
 			if ($metabyname_memcache) {
+				// @todo why name_id? is that even populated?
 				$metabyname_memcache->delete("{$obj->entity_guid}:{$obj->name_id}");
 			}
 		}
diff --git a/engine/lib/navigation.php b/engine/lib/navigation.php
index 86624cd7c..ab9cc05e8 100644
--- a/engine/lib/navigation.php
+++ b/engine/lib/navigation.php
@@ -126,6 +126,7 @@ function elgg_unregister_menu_item($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() == $item_name) {
 			return true;
 		}
@@ -216,7 +218,7 @@ function elgg_push_breadcrumb($title, $link = NULL) {
 	}
 
 	// avoid key collisions.
-	$CONFIG->breadcrumbs[] = array('title' => $title, 'link' => $link);
+	$CONFIG->breadcrumbs[] = array('title' => elgg_get_excerpt($title, 100), 'link' => $link);
 }
 
 /**
@@ -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()) {
 				$selected = true;
 				break 2;
@@ -321,7 +323,8 @@ function elgg_site_menu_setup($hook, $type, $return, $params) {
 	}
 	
 	if (!$selected) {
-		// nothing selected, match name to context
+		// nothing selected, match name to context or match url
+		$current_url = current_page_url();
 		foreach ($return as $section_name => $section) {
 			foreach ($section as $key => $item) {
 				// only highlight internal links
@@ -330,6 +333,10 @@ function elgg_site_menu_setup($hook, $type, $return, $params) {
 						$return[$section_name][$key]->setSelected(true);
 						break 2;
 					}
+					if ($item->getHref() == $current_url) {
+						$return[$section_name][$key]->setSelected(true);
+						break 2;
+					}
 				}
 			}
 		}
@@ -345,6 +352,7 @@ function elgg_site_menu_setup($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') && $item->annotation_id == 0) {
@@ -388,6 +396,7 @@ function elgg_entity_menu_setup($hook, $type, $return, $params) {
 	}
 	
 	$entity = $params['entity'];
+	/* @var ElggEntity $entity */
 	$handler = elgg_extract('handler', $params, false);
 
 	// access
@@ -433,6 +442,7 @@ 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);
 
 	$collapse = array(
@@ -481,6 +491,7 @@ function elgg_widget_menu_setup($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()) {
 		$url = elgg_http_add_url_query_elements('action/comments/delete', array(
diff --git a/engine/lib/notification.php b/engine/lib/notification.php
index 9e3c075a8..be0c359d4 100644
--- a/engine/lib/notification.php
+++ b/engine/lib/notification.php
@@ -86,7 +86,7 @@ function unregister_notification_handler($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($to)) {
@@ -110,12 +110,15 @@ function notify_user($to, $from, $subject, $message, array $params = NULL, $meth
 			// Are we overriding delivery?
 			$methods = $methods_override;
 			if (!$methods) {
-				$tmp = (array)get_user_notification_settings($guid);
+				$tmp = get_user_notification_settings($guid);
 				$methods = array();
-				foreach ($tmp as $k => $v) {
-					// Add method if method is turned on for user!
-					if ($v) {
-						$methods[] = $k;
+				// $tmp may be false. don't cast
+				if (is_object($tmp)) {
+					foreach ($tmp as $k => $v) {
+						// Add method if method is turned on for user!
+						if ($v) {
+							$methods[] = $k;
+						}
 					}
 				}
 			}
@@ -165,7 +168,7 @@ function notify_user($to, $from, $subject, $message, array $params = NULL, $meth
  *
  * @param int $user_guid The user id
  *
- * @return stdClass
+ * @return stdClass|false
  */
 function get_user_notification_settings($user_guid = 0) {
 	$user_guid = (int)$user_guid;
@@ -174,7 +177,8 @@ 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' => $user_guid,
 		'limit' => 0
@@ -237,6 +241,7 @@ function set_user_notification_setting($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 +268,7 @@ 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 +293,7 @@ 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 $params = NULL) {
@@ -344,6 +350,8 @@ function elgg_send_email($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 +430,7 @@ 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', $author_guid);
@@ -434,7 +442,7 @@ function register_notification_interest($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', $author_guid);
@@ -450,12 +458,13 @@ function remove_notification_interest($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, $NOTIFICATION_HANDLERS;
@@ -492,9 +501,10 @@ function object_notifications($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/opendd.php b/engine/lib/opendd.php
index f00ea6aab..7d635a295 100644
--- a/engine/lib/opendd.php
+++ b/engine/lib/opendd.php
@@ -7,6 +7,8 @@
  * @version 0.4
  */
 
+// @codingStandardsIgnoreStart
+
 /**
  * Attempt to construct an ODD object out of a XmlElement or sub-elements.
  *
@@ -103,3 +105,5 @@ function ODD_Import($xml) {
 function ODD_Export(ODDDocument $document) {
 	return "$document";
 }
+
+// @codingStandardsIgnoreEnd
diff --git a/engine/lib/output.php b/engine/lib/output.php
index 9295f2173..de4f911fb 100644
--- a/engine/lib/output.php
+++ b/engine/lib/output.php
@@ -12,29 +12,34 @@
  *
  * @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) {
+
+	// URI specification: http://www.ietf.org/rfc/rfc3986.txt
+	// This varies from the specification in the following ways:
+	//  * Supports non-ascii characters
+	//  * Does not allow parentheses and single quotes
+	//  * Cuts off commas, exclamation points, and periods off as last character
+
 	// @todo this causes problems with <attr = "val">
 	// must be in <attr="val"> format (no space).
 	// By default htmlawed rewrites tags to this format.
 	// if PHP supported conditional negative lookbehinds we could use this:
 	// $r = preg_replace_callback('/(?<!=)(?<![ ])?(?<!["\'])((ht|f)tps?:\/\/[^\s\r\n\t<>"\'\!\(\),]+)/i',
-	//
-	// we can put , in the list of excluded char but need to keep . because of domain names.
-	// it is removed in the callback.
-	$r = preg_replace_callback('/(?<!=)(?<!["\'])((ht|f)tps?:\/\/[^\s\r\n\t<>"\'\!\(\),]+)/i',
+	$r = preg_replace_callback('/(?<![=\/"\'])((ht|f)tps?:\/\/[^\s\r\n\t<>"\']+)/i',
 	create_function(
 		'$matches',
 		'
 			$url = $matches[1];
-			$period = \'\';
-			if (substr($url, -1, 1) == \'.\') {
-				$period = \'.\';
-				$url = trim($url, \'.\');
+			$punc = "";
+			$last = substr($url, -1, 1);
+			if (in_array($last, array(".", "!", ",", "(", ")"))) {
+				$punc = $last;
+				$url = rtrim($url, ".!,()");
 			}
 			$urltext = str_replace("/", "/<wbr />", $url);
-			return "<a href=\"$url\">$urltext</a>$period";
+			return "<a href=\"$url\" rel=\"nofollow\">$urltext</a>$punc";
 		'
 	), $text);
 
@@ -224,7 +229,6 @@ 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);
@@ -285,11 +289,9 @@ function elgg_get_friendly_title($title) {
 		return $result;
 	}
 
-	// handle some special cases
-	$title = str_replace('&amp;', 'and', $title);
-	// quotes and angle brackets stored in the database as html encoded
-	$title = htmlspecialchars_decode($title);
-
+	// titles are often stored HTML encoded
+	$title = html_entity_decode($title, ENT_QUOTES, 'UTF-8');
+	
 	$title = ElggTranslit::urlize($title);
 
 	return $title;
@@ -419,9 +421,28 @@ function _elgg_html_decode($string) {
 }
 
 /**
+ * Prepares query string for output to prevent CSRF attacks.
+ * 
+ * @param string $string
+ * @return string
+ *
+ * @access private
+ */
+function _elgg_get_display_query($string) {
+	//encode <,>,&, quotes and characters above 127
+	if (function_exists('mb_convert_encoding')) {

+		$display_query = mb_convert_encoding($string, 'HTML-ENTITIES', 'UTF-8');

+	} else {

+		// if no mbstring extension, we just strip characters

+		$display_query = preg_replace("/[^\x01-\x7F]/", "", $string);

+	}

+	return htmlspecialchars($display_query, ENT_QUOTES, 'UTF-8', false);
+}
+
+/**
  * 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  $params Params
diff --git a/engine/lib/pageowner.php b/engine/lib/pageowner.php
index 94765feee..bd63d08c6 100644
--- a/engine/lib/pageowner.php
+++ b/engine/lib/pageowner.php
@@ -29,7 +29,9 @@ function elgg_get_page_owner_guid($guid = 0) {
 	// return guid of page owner entity
 	$guid = elgg_trigger_plugin_hook('page_owner', 'system', NULL, 0);
 
-	$page_owner_guid = $guid;
+	if ($guid) {
+		$page_owner_guid = $guid;
+	}
 
 	return $guid;
 }
@@ -39,7 +41,7 @@ function elgg_get_page_owner_guid($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 +115,7 @@ function default_page_owner_handler($hook, $entity_type, $returnvalue, $params)
 		}
 
 		if ($user = get_user_by_username($username)) {
+			elgg_set_ignore_access($ia);
 			return $user->getGUID();
 		}
 	}
diff --git a/engine/lib/plugins.php b/engine/lib/plugins.php
index 94aff277e..d5d3db466 100644
--- a/engine/lib/plugins.php
+++ b/engine/lib/plugins.php
@@ -91,7 +91,9 @@ function elgg_get_plugin_ids_in_dir($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.
@@ -306,13 +311,11 @@ 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
-					| ELGG_PLUGIN_REGISTER_LANGUAGES
-					| ELGG_PLUGIN_REGISTER_CLASSES;
+	$start_flags = ELGG_PLUGIN_INCLUDE_START |
+					ELGG_PLUGIN_REGISTER_VIEWS |
+					ELGG_PLUGIN_REGISTER_LANGUAGES |
+					ELGG_PLUGIN_REGISTER_CLASSES;
 
 	if (!$plugins_path) {
 		return false;
@@ -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 int $user_guid Defaults to logged in user
- * @param str $plugin_id Defaults to contextual plugin name
+ * @param string $name      Name of the setting
+ * @param int    $user_guid Defaults to logged in user
+ * @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  $params Params
@@ -1102,6 +1105,49 @@ function plugins_test($hook, $type, $value, $params) {
 }
 
 /**
+ * Checks on deactivate plugin event if disabling it won't create unmet dependencies and blocks disable in such case.
+ *
+ * @param string $event  deactivate
+ * @param string $type   plugin
+ * @param array  $params Parameters array containing entry with ELggPlugin instance under 'plugin_entity' key
+ * @return bool  false to block plugin deactivation action
+ *
+ * @access private
+ */
+function _plugins_deactivate_dependency_check($event, $type, $params) {
+	$plugin_id = $params['plugin_entity']->getManifest()->getPluginID();
+	$plugin_name = $params['plugin_entity']->getManifest()->getName();
+
+	$active_plugins = elgg_get_plugins();
+
+	$dependents = array();
+	foreach ($active_plugins as $plugin) {
+		$manifest = $plugin->getManifest();
+		$requires = $manifest->getRequires();
+
+		foreach ($requires as $required) {
+			if ($required['type'] == 'plugin' && $required['name'] == $plugin_id) {
+				// there are active dependents
+				$dependents[$manifest->getPluginID()] = $plugin;
+			}
+		}
+	}
+
+	if ($dependents) {
+		$list = '<ul>';
+		// construct error message and prevent disabling
+		foreach ($dependents as $dependent) {
+			$list .= '<li>' . $dependent->getManifest()->getName() . '</li>';
+		}
+		$list .= '</ul>';
+
+		register_error(elgg_echo('ElggPlugin:Dependencies:ActiveDependent', array($plugin_name, $list)));
+
+		return false;
+	}
+}
+
+/**
  * Initialize the plugin system
  * Listens to system init and registers actions
  *
@@ -1112,6 +1158,10 @@ function plugin_init() {
 	run_function_once("plugin_run_once");
 
 	elgg_register_plugin_hook_handler('unit_test', 'system', 'plugins_test');
+	
+	// note - plugins are booted by the time this handler is registered
+	// deactivation due to error may have already occurred
+	elgg_register_event_handler('deactivate', 'plugin', '_plugins_deactivate_dependency_check');
 
 	elgg_register_action("plugins/settings/save", '', 'admin');
 	elgg_register_action("plugins/usersettings/save");
diff --git a/engine/lib/relationships.php b/engine/lib/relationships.php
index 01654b1ce..b0cd627fc 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
@@ -363,7 +363,7 @@ $relationship_guid = NULL, $inverse_relationship = FALSE) {
 /**
  * Returns a viewable list of entities by relationship
  *
- * @param array $options
+ * @param array $options Options array for retrieval of entities
  *
  * @see elgg_list_entities()
  * @see elgg_get_entities_from_relationship()
@@ -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..e92040eb7 100644
--- a/engine/lib/river.php
+++ b/engine/lib/river.php
@@ -120,7 +120,7 @@ $posted = 0, $annotation_id = 0) {
  *   subtypes             => STR|ARR Entity subtype string(s)
  *   type_subtype_pairs   => ARR     Array of type => subtype pairs where subtype
  *                                   can be an array of subtype strings
- * 
+ *
  *   posted_time_lower    => INT     The lower bound on the time posted
  *   posted_time_upper    => INT     The upper bound on the time posted
  *
@@ -380,10 +380,10 @@ function _elgg_prefetch_river_entities(array $river_items) {
 	// prefetch objects and subjects
 	$guids = array();
 	foreach ($river_items as $item) {
-		if ($item->subject_guid && !retrieve_cached_entity($item->subject_guid)) {
+		if ($item->subject_guid && !_elgg_retrieve_cached_entity($item->subject_guid)) {
 			$guids[$item->subject_guid] = true;
 		}
-		if ($item->object_guid && !retrieve_cached_entity($item->object_guid)) {
+		if ($item->object_guid && !_elgg_retrieve_cached_entity($item->object_guid)) {
 			$guids[$item->object_guid] = true;
 		}
 	}
@@ -402,7 +402,7 @@ function _elgg_prefetch_river_entities(array $river_items) {
 	$guids = array();
 	foreach ($river_items as $item) {
 		$object = $item->getObjectEntity();
-		if ($object->container_guid && !retrieve_cached_entity($object->container_guid)) {
+		if ($object->container_guid && !_elgg_retrieve_cached_entity($object->container_guid)) {
 			$guids[$object->container_guid] = true;
 		}
 	}
@@ -434,8 +434,13 @@ function elgg_list_river(array $options = array()) {
 		'pagination' => TRUE,
 		'list_class' => 'elgg-list-river elgg-river', // @todo remove elgg-river in Elgg 1.9
 	);
-
+	
 	$options = array_merge($defaults, $options);
+	
+	if (!$options["limit"] && !$options["offset"]) {

+		// no need for pagination if listing is unlimited

+		$options["pagination"] = false;

+	}
 
 	$options['count'] = TRUE;
 	$count = elgg_get_river($options);
@@ -445,6 +450,7 @@ function elgg_list_river(array $options = array()) {
 
 	$options['count'] = $count;
 	$options['items'] = $items;
+	
 	return elgg_view('page/components/list', $options);
 }
 
@@ -500,6 +506,7 @@ function elgg_get_river_type_subtype_where_sql($table, $types, $subtypes, $pairs
 		return '';
 	}
 
+	$wheres = array();
 	$types_wheres = array();
 	$subtypes_wheres = array();
 
@@ -644,7 +651,7 @@ function update_river_access_by_object($object_guid, $access_id) {
 }
 
 /**
- * Page handler for activiy
+ * Page handler for activity
  *
  * @param array $page
  * @return bool
@@ -663,10 +670,6 @@ function elgg_river_page_handler($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..e3d5ce9cd 100644
--- a/engine/lib/sessions.php
+++ b/engine/lib/sessions.php
@@ -87,6 +87,9 @@ function elgg_is_admin_logged_in() {
  */
 function elgg_is_admin_user($user_guid) {
 	global $CONFIG;
+
+	$user_guid = (int)$user_guid;
+
 	// cannot use magic metadata here because of recursion
 
 	// must support the old way of getting admin from metadata
@@ -286,8 +289,6 @@ 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'));
@@ -325,6 +326,12 @@ function login(ElggUser $user, $persistent = false) {
 	set_last_login($_SESSION['guid']);
 	reset_login_failure_count($user->guid); // Reset any previous failed login attempts
 
+	// if memcache is enabled, invalidate the user in memcache @see https://github.com/Elgg/Elgg/issues/3143
+	if (is_memcache_available()) {
+		// this needs to happen with a shutdown function because of the timing with set_last_login()
+		register_shutdown_function("_elgg_invalidate_memcache_for_entity", $_SESSION['guid']);
+	}
+	
 	return true;
 }
 
@@ -334,8 +341,6 @@ function login(ElggUser $user, $persistent = false) {
  * @return bool
  */
 function logout() {
-	global $CONFIG;
-
 	if (isset($_SESSION['user'])) {
 		if (!elgg_trigger_event('logout', 'user', $_SESSION['user'])) {
 			return false;
@@ -616,10 +621,8 @@ function _elgg_session_destroy($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  $params Params
diff --git a/engine/lib/statistics.php b/engine/lib/statistics.php
index 5ee640549..4cb0bb0b8 100644
--- a/engine/lib/statistics.php
+++ b/engine/lib/statistics.php
@@ -95,15 +95,20 @@ function get_number_users($show_deactivated = false) {
  * @return string
   */
 function get_online_users() {
-	$count = find_active_users(600, 10, 0, true);
-	$objects = find_active_users(600, 10);
+	$limit = max(0, (int) get_input("limit", 10));
+	$offset = max(0, (int) get_input("offset", 0));
+	
+	$count = find_active_users(600, $limit, $offset, true);
+	$objects = find_active_users(600, $limit, $offset);
 
 	if ($objects) {
 		return elgg_view_entity_list($objects, array(
 			'count' => $count,
-			'limit' => 10
+			'limit' => $limit,
+			'offset' => $offset
 		));
 	}
+	return '';
 }
 
 /**
diff --git a/engine/lib/system_log.php b/engine/lib/system_log.php
index 53fa24557..84302632e 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 $object */
 		if (datalist_get('version') < 2012012000) {
 			// this is a site that doesn't have the ip_address column yet
 			return;
@@ -184,7 +187,16 @@ function system_log($object, $event) {
 		$object_subtype = $object->getSubtype();
 		$event = sanitise_string($event);
 		$time = time();
-		$ip_address = sanitise_string($_SERVER['REMOTE_ADDR']);
+
+		if (!empty($_SERVER['HTTP_X_FORWARDED_FOR'])) {
+			$ip_address = array_pop(explode(',', $_SERVER['HTTP_X_FORWARDED_FOR']));
+		} elseif (!empty($_SERVER['HTTP_X_REAL_IP'])) {
+			$ip_address = array_pop(explode(',', $_SERVER['HTTP_X_REAL_IP']));
+		} else {
+			$ip_address = $_SERVER['REMOTE_ADDR'];
+		}
+		$ip_address = sanitise_string($ip_address);
+
 		$performed_by = elgg_get_logged_in_user_guid();
 
 		if (isset($object->access_id)) {
diff --git a/engine/lib/tags.php b/engine/lib/tags.php
index a0887d0f3..586a9b9e4 100644
--- a/engine/lib/tags.php
+++ b/engine/lib/tags.php
@@ -48,7 +48,7 @@ function calculate_tag_size($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..158ec9ec1 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();
@@ -244,7 +245,7 @@ function version_upgrade() {
 
 	// No version number? Oh snap...this is an upgrade from a clean installation < 1.7.
 	// Run all upgrades without error reporting and hope for the best.
-	// See http://trac.elgg.org/elgg/ticket/1432 for more.
+	// See https://github.com/elgg/elgg/issues/1432 for more.
 	$quiet = !$dbversion;
 
 	// Note: Database upgrades are deprecated as of 1.8.  Use code upgrades.  See #1433
@@ -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();
 
@@ -354,15 +354,12 @@ function _elgg_upgrade_unlock() {
  * @access private
  */
 function _elgg_upgrade_is_locked() {
-	global $CONFIG, $DB_QUERY_CACHE;
-	
+	global $CONFIG;
+
 	$is_locked = count(get_data("show tables like '{$CONFIG->dbprefix}upgrade_lock'"));
-	
-	// Invalidate query cache
-	if ($DB_QUERY_CACHE) {
-		$DB_QUERY_CACHE->clear();
-		elgg_log("Query cache invalidated", 'NOTICE');
-	}
-	
+
+	// @todo why?
+	_elgg_invalidate_query_cache();
+
 	return $is_locked;
 }
diff --git a/engine/lib/upgrades/2009102801.php b/engine/lib/upgrades/2009102801.php
index cab9a6835..3ad113fb2 100644
--- a/engine/lib/upgrades/2009102801.php
+++ b/engine/lib/upgrades/2009102801.php
@@ -203,14 +203,15 @@ function user_file_matrix($guid) {
 	return "$time_created/$user->guid/";
 }
 
-global $DB_QUERY_CACHE, $DB_PROFILE, $ENTITY_CACHE;
+global $ENTITY_CACHE, $CONFIG;
 /**
  * Upgrade file locations
  */
 $users = mysql_query("SELECT guid, username
 	FROM {$CONFIG->dbprefix}users_entity WHERE username != ''");
 while ($user = mysql_fetch_object($users)) {
-	$DB_QUERY_CACHE = $DB_PROFILE = $ENTITY_CACHE = array();
+	$ENTITY_CACHE = array();
+	_elgg_invalidate_query_cache();
 
 	$to = $CONFIG->dataroot . user_file_matrix($user->guid);
 	foreach (array('1_0', '1_1', '1_6') as $version) {
diff --git a/engine/lib/upgrades/2010033101.php b/engine/lib/upgrades/2010033101.php
index 0bffee001..4779295fd 100644
--- a/engine/lib/upgrades/2010033101.php
+++ b/engine/lib/upgrades/2010033101.php
@@ -1,7 +1,7 @@
 <?php
 
 /**
- * Conditional upgrade for UTF8 as described in http://trac.elgg.org/ticket/1928
+ * Conditional upgrade for UTF8 as described in https://github.com/elgg/elgg/issues/1928
  */
 
 // get_version() returns the code version.
diff --git a/engine/lib/upgrades/2010061501.php b/engine/lib/upgrades/2010061501.php
index 9ff7d3102..744c28fd5 100644
--- a/engine/lib/upgrades/2010061501.php
+++ b/engine/lib/upgrades/2010061501.php
@@ -45,7 +45,7 @@ if ($dbversion < 2009100701) {
 			}
 		}
 
-		global $DB_QUERY_CACHE, $DB_PROFILE, $ENTITY_CACHE;
+		global $ENTITY_CACHE;
 
 		/**
 			Upgrade file locations
@@ -60,7 +60,9 @@ if ($dbversion < 2009100701) {
 		$users = mysql_query("SELECT guid, username FROM {$CONFIG->dbprefix}users_entity
 			WHERE username != ''", $link);
 		while ($user = mysql_fetch_object($users)) {
-			$DB_QUERY_CACHE = $DB_PROFILE = $ENTITY_CACHE = array();
+			$ENTITY_CACHE = array();
+			_elgg_invalidate_query_cache();
+
 
 			$to = $CONFIG->dataroot . user_file_matrix($user->guid);
 			foreach (array('1_0', '1_1', '1_6') as $version) {
diff --git a/engine/lib/upgrades/2010071001.php b/engine/lib/upgrades/2010071001.php
index 1b5d379d8..5594493a8 100644
--- a/engine/lib/upgrades/2010071001.php
+++ b/engine/lib/upgrades/2010071001.php
@@ -30,11 +30,12 @@ function user_file_matrix_2010071001($guid) {
 
 $sizes = array('large', 'medium', 'small', 'tiny', 'master', 'topbar');
 
-global $DB_QUERY_CACHE, $DB_PROFILE, $ENTITY_CACHE, $CONFIG;
+global $ENTITY_CACHE, $CONFIG;
 $users = mysql_query("SELECT guid, username FROM {$CONFIG->dbprefix}users_entity
 	WHERE username != ''");
 while ($user = mysql_fetch_object($users)) {
-	$DB_QUERY_CACHE = $DB_PROFILE = $ENTITY_CACHE = array();
+	$ENTITY_CACHE = array();
+	_elgg_invalidate_query_cache();
 
 	$user_directory = user_file_matrix_2010071001($user->guid);
 	if (!$user_directory) {
diff --git a/engine/lib/upgrades/2010071002.php b/engine/lib/upgrades/2010071002.php
index 30bd6538c..52aa15ef5 100644
--- a/engine/lib/upgrades/2010071002.php
+++ b/engine/lib/upgrades/2010071002.php
@@ -4,12 +4,13 @@
  */
 
 // loop through all users checking collections and notifications
-global $DB_QUERY_CACHE, $DB_PROFILE, $ENTITY_CACHE, $CONFIG;
+global $ENTITY_CACHE, $CONFIG;
 global $NOTIFICATION_HANDLERS;
 $users = mysql_query("SELECT guid, username FROM {$CONFIG->dbprefix}users_entity
 	WHERE username != ''");
 while ($user = mysql_fetch_object($users)) {
-	$DB_QUERY_CACHE = $DB_PROFILE = $ENTITY_CACHE = array();
+	$ENTITY_CACHE = array();
+	_elgg_invalidate_query_cache();
 
 	$user = get_entity($user->guid);
 	foreach ($NOTIFICATION_HANDLERS as $method => $foo) {
diff --git a/engine/lib/upgrades/2011052801.php b/engine/lib/upgrades/2011052801.php
index 8084bc06c..b5a8e1018 100644
--- a/engine/lib/upgrades/2011052801.php
+++ b/engine/lib/upgrades/2011052801.php
@@ -2,7 +2,7 @@
 /**
  * Make sure all users have the relationship member_of_site
  */
-global $DB_QUERY_CACHE, $DB_PROFILE, $ENTITY_CACHE, $CONFIG;
+global $ENTITY_CACHE;
 $db_prefix = get_config('dbprefix');
 
 $limit = 100;
@@ -17,7 +17,8 @@ $q = "SELECT e.* FROM {$db_prefix}entities e
 $users = get_data($q);
 
 while ($users) {
-	$DB_QUERY_CACHE = $DB_PROFILE = $ENTITY_CACHE = array();
+	$ENTITY_CACHE = array();
+	_elgg_invalidate_query_cache();
 
 	// do manually to not trigger any events because these aren't new users.
 	foreach ($users as $user) {
diff --git a/engine/lib/upgrades/2012041801-1.8.3-multiple_user_tokens-852225f7fd89f6c5.php b/engine/lib/upgrades/2012041801-1.8.3-multiple_user_tokens-852225f7fd89f6c5.php
index 07732f261..780038c32 100644
--- a/engine/lib/upgrades/2012041801-1.8.3-multiple_user_tokens-852225f7fd89f6c5.php
+++ b/engine/lib/upgrades/2012041801-1.8.3-multiple_user_tokens-852225f7fd89f6c5.php
@@ -3,7 +3,7 @@
  * Elgg 1.8.3 upgrade 2012041801
  * multiple_user_tokens
  *
- * Fixes http://trac.elgg.org/ticket/4291
+ * Fixes https://github.com/elgg/elgg/issues/4291
  * Removes the unique index on users_apisessions for user_guid and site_guid
  */
 
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..8eccf05e2
--- /dev/null
+++ b/engine/lib/upgrades/2013030600-1.8.13-update_user_location-8999eb8bf1bdd9a3.php
@@ -0,0 +1,24 @@
+<?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.
+ */
+
+$ia = elgg_set_ignore_access(true);
+$options = array(
+	'type' => 'user',
+	'limit' => 0,
+);
+$batch = new ElggBatch('elgg_get_entities', $options);
+
+foreach ($batch as $entity) {
+	_elgg_invalidate_query_cache();
+	
+	if (is_array($entity->location)) {
+		$entity->location = implode(', ', $entity->location);
+	}
+}
+elgg_set_ignore_access($ia);
diff --git a/engine/lib/upgrades/2013051700-1.8.15-add_missing_group_index-52a63a3a3ffaced2.php b/engine/lib/upgrades/2013051700-1.8.15-add_missing_group_index-52a63a3a3ffaced2.php
new file mode 100644
index 000000000..ee99bdbc8
--- /dev/null
+++ b/engine/lib/upgrades/2013051700-1.8.15-add_missing_group_index-52a63a3a3ffaced2.php
@@ -0,0 +1,28 @@
+<?php
+/**
+ * Elgg 1.8.15 upgrade 2013051700
+ * add_missing_group_index
+ *
+ * Some Elgg sites are missing the groups_entity full text index on name and
+ * description. This checks if it exists and adds it if it does not.
+ */
+
+$db_prefix = elgg_get_config('dbprefix');
+
+$full_text_index_exists = false;
+$results = get_data("SHOW INDEX FROM {$db_prefix}groups_entity");
+if ($results) {
+	foreach ($results as $result) {
+		if ($result->Index_type === 'FULLTEXT') {
+			$full_text_index_exists = true;
+		}
+	}
+}
+
+if ($full_text_index_exists == false) {
+	$query = "ALTER TABLE {$db_prefix}groups_entity 
+		ADD FULLTEXT name_2 (name, description)";
+	if (!update_data($query)) {
+		elgg_log("Failed to add full text index to groups_entity table", 'ERROR');
+	}
+}
diff --git a/engine/lib/upgrades/2013052900-1.8.15-ipv6_in_syslog-f5c2cc0196e9e731.php b/engine/lib/upgrades/2013052900-1.8.15-ipv6_in_syslog-f5c2cc0196e9e731.php
new file mode 100644
index 000000000..d333a6cd2
--- /dev/null
+++ b/engine/lib/upgrades/2013052900-1.8.15-ipv6_in_syslog-f5c2cc0196e9e731.php
@@ -0,0 +1,12 @@
+<?php
+/**
+ * Elgg 1.8.15 upgrade 2013052900
+ * ipv6_in_syslog
+ *
+ * Upgrade the ip column in system_log to be able to store ipv6 addresses
+ */
+
+$db_prefix = elgg_get_config('dbprefix');
+$q = "ALTER TABLE {$db_prefix}system_log MODIFY COLUMN ip_address varchar(46) NOT NULL";
+
+update_data($q);
\ No newline at end of file
diff --git a/engine/lib/upgrades/2013060900-1.8.15-site_secret-404fc165cf9e0ac9.php b/engine/lib/upgrades/2013060900-1.8.15-site_secret-404fc165cf9e0ac9.php
new file mode 100644
index 000000000..538d74dd6
--- /dev/null
+++ b/engine/lib/upgrades/2013060900-1.8.15-site_secret-404fc165cf9e0ac9.php
@@ -0,0 +1,16 @@
+<?php
+/**
+ * Elgg 1.8.15 upgrade 2013060900
+ * site_secret
+ *
+ * Description
+ */
+
+$strength = _elgg_get_site_secret_strength();
+
+if ($strength !== 'strong') {
+	// a new key is needed immediately
+	register_translations(elgg_get_root_path() . 'languages/');
+
+	elgg_add_admin_notice('weak_site_key', elgg_echo("upgrade:site_secret_warning:$strength"));
+}
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..0e36dc46d 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") {
 		$params = array(
 			'name' => '1_account',
 			'text' => elgg_echo('usersettings:user:opt:linktext'),
@@ -308,7 +308,7 @@ function usersettings_page_handler($page) {
 		$user = get_user_by_username($page[1]);
 		elgg_set_page_owner_guid($user->guid);
 	} else {
-		$user = elgg_get_logged_in_user_guid();
+		$user = elgg_get_logged_in_user_entity();
 		elgg_set_page_owner_guid($user->guid);
 	}
 
@@ -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..a8fb9121c 100644
--- a/engine/lib/users.php
+++ b/engine/lib/users.php
@@ -237,7 +237,7 @@ function make_user_admin($user_guid) {
 			}
 
 			$r = update_data("UPDATE {$CONFIG->dbprefix}users_entity set admin='yes' where guid=$user_guid");
-			invalidate_cache_for_entity($user_guid);
+			_elgg_invalidate_cache_for_entity($user_guid);
 			return $r;
 		}
 
@@ -273,7 +273,7 @@ function remove_user_admin($user_guid) {
 			}
 
 			$r = update_data("UPDATE {$CONFIG->dbprefix}users_entity set admin='no' where guid=$user_guid");
-			invalidate_cache_for_entity($user_guid);
+			_elgg_invalidate_cache_for_entity($user_guid);
 			return $r;
 		}
 
@@ -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, $timeupper = 0) {
@@ -555,13 +553,18 @@ function get_user($guid) {
 function get_user_by_username($username) {
 	global $CONFIG, $USERNAME_TO_GUID_MAP_CACHE;
 
+	// Fixes #6052. Username is frequently sniffed from the path info, which,
+	// unlike $_GET, is not URL decoded. If the username was not URL encoded,
+	// this is harmless.
+	$username = rawurldecode($username);
+
 	$username = sanitise_string($username);
 	$access = get_access_sql_suffix('e');
 
 	// Caching
 	if ((isset($USERNAME_TO_GUID_MAP_CACHE[$username]))
-	&& (retrieve_cached_entity($USERNAME_TO_GUID_MAP_CACHE[$username]))) {
-		return retrieve_cached_entity($USERNAME_TO_GUID_MAP_CACHE[$username]);
+			&& (_elgg_retrieve_cached_entity($USERNAME_TO_GUID_MAP_CACHE[$username]))) {
+		return _elgg_retrieve_cached_entity($USERNAME_TO_GUID_MAP_CACHE[$username]);
 	}
 
 	$query = "SELECT e.* from {$CONFIG->dbprefix}users_entity u
@@ -594,9 +597,9 @@ function get_user_by_code($code) {
 
 	// Caching
 	if ((isset($CODE_TO_GUID_MAP_CACHE[$code]))
-	&& (retrieve_cached_entity($CODE_TO_GUID_MAP_CACHE[$code]))) {
+	&& (_elgg_retrieve_cached_entity($CODE_TO_GUID_MAP_CACHE[$code]))) {
 
-		return retrieve_cached_entity($CODE_TO_GUID_MAP_CACHE[$code]);
+		return _elgg_retrieve_cached_entity($CODE_TO_GUID_MAP_CACHE[$code]);
 	}
 
 	$query = "SELECT e.* from {$CONFIG->dbprefix}users_entity u
@@ -675,25 +678,22 @@ 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;
@@ -710,19 +710,18 @@ function send_new_password_request($user_guid) {
  * @return bool
  */
 function force_user_password_reset($user_guid, $password) {
-	global $CONFIG;
-
 	$user = get_entity($user_guid);
+	if ($user instanceof ElggUser) {
+		$ia = elgg_set_ignore_access();
 
-	if ($user) {
-		$salt = generate_random_cleartext_password(); // Reset the salt
-		$user->salt = $salt;
+		$user->salt = generate_random_cleartext_password();
+		$hash = generate_user_password($user, $password);		
+		$user->password = $hash;
+		$result = (bool)$user->save();
 
-		$hash = generate_user_password($user, $password);
+		elgg_set_ignore_access($ia);
 
-		$query = "UPDATE {$CONFIG->dbprefix}users_entity
-			set password='$hash', salt='$salt' where guid=$user_guid";
-		return update_data($query);
+		return $result;
 	}
 
 	return false;
@@ -742,7 +741,7 @@ 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 == $conf_code) {
@@ -756,7 +755,7 @@ function execute_new_password_request($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'), $email, array(), 'email');
 			}
 		}
 	}
@@ -841,7 +840,7 @@ function validate_username($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($msg);
 		}
 	}
@@ -908,13 +907,11 @@ function validate_email_address($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 +1028,7 @@ function elgg_get_user_validation_status($user_guid) {
 		'metadata_name' => 'validated'
 	));
 	if ($md == false) {
-		return;
+		return null;
 	}
 
 	if ($md[0]->value) {
@@ -1067,10 +1064,10 @@ function collections_submenu_items() {
  * @return bool
  * @access private
  */
-function friends_page_handler($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($user->getGUID());
 	}
 	if (elgg_get_logged_in_user_guid() == elgg_get_page_owner_guid()) {
@@ -1099,6 +1096,7 @@ function friends_page_handler($page_elements, $handler) {
  * @access private
  */
 function collections_page_handler($page_elements) {
+	gatekeeper();
 	elgg_set_context('friends');
 	$base = elgg_get_config('path');
 	if (isset($page_elements[0])) {
@@ -1197,13 +1195,11 @@ 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 +1229,7 @@ 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() != $user->guid) {
@@ -1309,7 +1306,12 @@ function elgg_user_hover_menu($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, $params) {
@@ -1321,6 +1323,7 @@ function elgg_users_setup_entity_menu($hook, $type, $return, $params) {
 	if (!elgg_instanceof($entity, 'user')) {
 		return $return;
 	}
+	/* @var ElggUser $entity */
 
 	if ($entity->isBanned()) {
 		$banned = elgg_echo('banned');
@@ -1334,9 +1337,10 @@ function elgg_users_setup_entity_menu($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 +1591,7 @@ 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  $params Params
diff --git a/engine/lib/views.php b/engine/lib/views.php
index 01291b889..1142461fe 100644
--- a/engine/lib/views.php
+++ b/engine/lib/views.php
@@ -218,7 +218,7 @@ function elgg_register_ajax_view($view) {
 
 /**
  * Unregister a view for ajax calls
- * 
+ *
  * @param string $view The view name
  * @return void
  * @since 1.8.3
@@ -369,7 +369,7 @@ function elgg_view_exists($view, $viewtype = '', $recurse = true) {
  * view, $view_name plugin hook.
  *
  * @warning Any variables in $_SESSION will override passed vars
- * upon name collision.  See {@trac #2124}.
+ * upon name collision.  See https://github.com/Elgg/Elgg/issues/2124
  *
  * @param string  $view     The name and location of the view to use
  * @param array   $vars     Variables to pass to the view.
@@ -795,7 +795,7 @@ function elgg_view_menu($menu_name, array $vars = array()) {
  *  - bool 'full_view' Whether to show a full or condensed view.
  *
  * @tip This function can automatically appends annotations to entities if in full
- * view and a handler is registered for the entity:annotate.  See {@trac 964} and
+ * view and a handler is registered for the entity:annotate.  See https://github.com/Elgg/Elgg/issues/964 and
  * {@link elgg_view_entity_annotations()}.
  *
  * @param ElggEntity $entity The entity to display
@@ -992,6 +992,11 @@ function elgg_view_annotation(ElggAnnotation $annotation, array $vars = array(),
 function elgg_view_entity_list($entities, $vars = array(), $offset = 0, $limit = 10, $full_view = true,
 $list_type_toggle = true, $pagination = true) {
 
+	if (!$vars["limit"] && !$vars["offset"]) {
+		// no need for pagination if listing is unlimited

+		$vars["pagination"] = false;

+	}

+		
 	if (!is_int($offset)) {
 		$offset = (int)get_input('offset', 0);
 	}
@@ -1064,8 +1069,13 @@ function elgg_view_annotation_list($annotations, array $vars = array()) {
 		'full_view' => true,
 		'offset_key' => 'annoff',
 	);
-
+	
 	$vars = array_merge($defaults, $vars);
+	
+	if (!$vars["limit"] && !$vars["offset"]) {

+		// no need for pagination if listing is unlimited

+		$vars["pagination"] = false;

+	}
 
 	return elgg_view('page/components/list', $vars);
 }
@@ -1107,7 +1117,7 @@ function elgg_view_entity_annotations(ElggEntity $entity, $full_view = true) {
  * This is a shortcut for {@elgg_view page/elements/title}.
  *
  * @param string $title The page title
- * @param array $vars   View variables (was submenu be displayed? (deprecated))
+ * @param array  $vars  View variables (was submenu be displayed? (deprecated))
  *
  * @return string The HTML (etc)
  */
@@ -1179,7 +1189,7 @@ function elgg_view_comments($entity, $add_comment = true, array $vars = array())
  *
  * @param string $image The icon and other information
  * @param string $body  Description content
- * @param array $vars   Additional parameters for the view
+ * @param array  $vars  Additional parameters for the view
  *
  * @return string
  * @since 1.8.0
@@ -1236,15 +1246,17 @@ function elgg_view_river_item($item, array $vars = array()) {
 		// subject is disabled or subject/object deleted
 		return '';
 	}
+
+	// @todo this needs to be cleaned up
 	// Don't hide objects in closed groups that a user can see.
-	// see http://trac.elgg.org/ticket/4789
-//	else {
-//		// hide based on object's container
-//		$visibility = ElggGroupItemVisibility::factory($object->container_guid);
-//		if ($visibility->shouldHideItems) {
-//			return '';
-//		}
-//	}
+	// see https://github.com/elgg/elgg/issues/4789
+	//	else {
+	//		// hide based on object's container
+	//		$visibility = ElggGroupItemVisibility::factory($object->container_guid);
+	//		if ($visibility->shouldHideItems) {
+	//			return '';
+	//		}
+	//	}
 
 	$vars['item'] = $item;
 
@@ -1308,7 +1320,7 @@ 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  $vars Additional parameters for the rendering
  *
  * @return string
@@ -1332,12 +1344,12 @@ function elgg_view_list_item($item, array $vars = array()) {
 
 /**
  * View one of the elgg sprite icons
- * 
+ *
  * Shorthand for <span class="elgg-icon elgg-icon-$name"></span>
- * 
+ *
  * @param string $name  The specific icon to display
  * @param string $class Additional class: float, float-alt, or custom class
- * 
+ *
  * @return string The html for displaying an icon
  */
 function elgg_view_icon($name, $class = '') {
@@ -1451,17 +1463,13 @@ function elgg_get_views($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];
@@ -1640,7 +1648,7 @@ function elgg_views_boot() {
 	}
 
 	// set default icon sizes - can be overridden in settings.php or with plugin
-	if (!$CONFIG->icon_sizes) {
+	if (!isset($CONFIG->icon_sizes)) {
 		$icon_sizes = array(
 			'topbar' => array('w' => 16, 'h' => 16, 'square' => TRUE, 'upscale' => TRUE),
 			'tiny' => array('w' => 25, 'h' => 25, 'square' => TRUE, 'upscale' => TRUE),
diff --git a/engine/lib/web_services.php b/engine/lib/web_services.php
index c8e4a13cc..51cad6f39 100644
--- a/engine/lib/web_services.php
+++ b/engine/lib/web_services.php
@@ -178,7 +178,7 @@ function authenticate_method($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);
 		}
 	}
 
@@ -1166,6 +1166,17 @@ function list_all_apis() {
  * @access private
  */
 function auth_gettoken($username, $password) {
+	// check if username is an email address

+	if (is_email_address($username)) {

+		$users = get_user_by_email($username);

+			

+		// check if we have a unique user

+		if (is_array($users) && (count($users) == 1)) {

+			$username = $users[0]->username;

+		}

+	}

+	

+	// validate username and password
 	if (true === elgg_authenticate($username, $password)) {
 		$token = create_user_token($username);
 		if ($token) {
@@ -1195,7 +1206,7 @@ $ERRORS = array();
  *
  * @return void
  * @access private
- * 
+ *
  * @throws Exception
  */
 function _php_api_error_handler($errno, $errmsg, $filename, $linenum, $vars) {
@@ -1267,14 +1278,14 @@ function service_handler($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/schema/mysql.sql b/engine/schema/mysql.sql
index 6c6e9db89..4714b71bb 100644
--- a/engine/schema/mysql.sql
+++ b/engine/schema/mysql.sql
@@ -361,7 +361,7 @@ CREATE TABLE `prefix_system_log` (
   `access_id` int(11) NOT NULL,
   `enabled` enum('yes','no') NOT NULL DEFAULT 'yes',
   `time_created` int(11) NOT NULL,
-  `ip_address` varchar(15) NOT NULL,
+  `ip_address` varchar(46) NOT NULL,
   PRIMARY KEY (`id`),
   KEY `object_id` (`object_id`),
   KEY `object_class` (`object_class`),
diff --git a/engine/tests/api/access_collections.php b/engine/tests/api/access_collections.php
index ebcd7d318..4acfae596 100644
--- a/engine/tests/api/access_collections.php
+++ b/engine/tests/api/access_collections.php
@@ -54,7 +54,6 @@ class ElggCoreAccessCollectionsTest extends ElggCoreUnitTest {
 	}
 
 	public function testCreateGetDeleteACL() {
-		global $DB_QUERY_CACHE;
 		
 		$acl_name = 'test access collection';
 		$acl_id = create_access_collection($acl_name);
@@ -67,8 +66,6 @@ class ElggCoreAccessCollectionsTest extends ElggCoreUnitTest {
 		$this->assertEqual($acl->id, $acl_id);
 
 		if ($acl) {
-			$DB_QUERY_CACHE = array();
-			
 			$this->assertEqual($acl->name, $acl_name);
 
 			$result = delete_access_collection($acl_id);
diff --git a/engine/tests/api/annotations.php b/engine/tests/api/annotations.php
index 947292970..c0b0687cc 100644
--- a/engine/tests/api/annotations.php
+++ b/engine/tests/api/annotations.php
@@ -65,6 +65,86 @@ class ElggCoreAnnotationAPITest extends ElggCoreUnitTest {
 		$annotations = elgg_get_annotations($options);
 		$this->assertTrue(empty($annotations));
 
+		// nothing to delete so null returned
+		$this->assertNull(elgg_delete_annotations($options));
+
+		$this->assertTrue($e->delete());
+	}
+
+	public function testElggDisableAnnotations() {
+		$e = new ElggObject();
+		$e->save();
+
+		for ($i=0; $i<30; $i++) {
+			$e->annotate('test_annotation', rand(0,10000));
+		}
+
+		$options = array(
+			'guid' => $e->getGUID(),
+			'limit' => 0
+		);
+
+		$this->assertTrue(elgg_disable_annotations($options));
+
+		$annotations = elgg_get_annotations($options);
+		$this->assertTrue(empty($annotations));
+
+		access_show_hidden_entities(true);
+		$annotations = elgg_get_annotations($options);
+		$this->assertIdentical(30, count($annotations));
+		access_show_hidden_entities(false);
+
+		$this->assertTrue($e->delete());
+	}
+
+	public function testElggEnableAnnotations() {
+		$e = new ElggObject();
+		$e->save();
+
+		for ($i=0; $i<30; $i++) {
+			$e->annotate('test_annotation', rand(0,10000));
+		}
+
+		$options = array(
+			'guid' => $e->getGUID(),
+			'limit' => 0
+		);
+
+		$this->assertTrue(elgg_disable_annotations($options));
+
+		// cannot see any annotations so returns null
+		$this->assertNull(elgg_enable_annotations($options));
+
+		access_show_hidden_entities(true);
+		$this->assertTrue(elgg_enable_annotations($options));
+		access_show_hidden_entities(false);
+
+		$annotations = elgg_get_annotations($options);
+		$this->assertIdentical(30, count($annotations));
+
+		$this->assertTrue($e->delete());
+	}
+
+	public function testElggAnnotationExists() {
+		$e = new ElggObject();
+		$e->save();
+		$guid = $e->getGUID();
+
+		$this->assertFalse(elgg_annotation_exists($guid, 'test_annotation'));
+
+		$e->annotate('test_annotation', rand(0, 10000));
+		$this->assertTrue(elgg_annotation_exists($guid, 'test_annotation'));
+		// this metastring should always exist but an annotation of this name should not
+		$this->assertFalse(elgg_annotation_exists($guid, 'email'));
+
+		$options = array(
+			'guid' => $guid,
+			'limit' => 0
+		);
+		$this->assertTrue(elgg_disable_annotations($options));
+		$this->assertTrue(elgg_annotation_exists($guid, 'test_annotation'));
+
 		$this->assertTrue($e->delete());
+		$this->assertFalse(elgg_annotation_exists($guid, 'test_annotation'));
 	}
 }
diff --git a/engine/tests/api/entity_getter_functions.php b/engine/tests/api/entity_getter_functions.php
index 9db248de9..fef9dc0c5 100644
--- a/engine/tests/api/entity_getter_functions.php
+++ b/engine/tests/api/entity_getter_functions.php
@@ -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,
+		);
+		$count = elgg_get_entities_from_annotation_calculation($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));
+	}
 }
diff --git a/engine/tests/api/helpers.php b/engine/tests/api/helpers.php
index 62e4471e0..414fb4145 100644
--- a/engine/tests/api/helpers.php
+++ b/engine/tests/api/helpers.php
@@ -519,7 +519,7 @@ class ElggCoreHelpersTest extends ElggCoreUnitTest {
 		$this->assertIdentical($elements_sorted_string, $test_elements);
 	}
 
-	// see http://trac.elgg.org/ticket/4288
+	// see https://github.com/elgg/elgg/issues/4288
 	public function testElggBatchIncOffset() {
 		// normal increment
 		$options = array(
@@ -578,6 +578,107 @@ class ElggCoreHelpersTest extends ElggCoreUnitTest {
 		$this->assertEqual(11, $j);
 	}
 
+	public function testElggBatchReadHandlesBrokenEntities() {
+		$num_test_entities = 8;
+		$guids = array();
+		for ($i = $num_test_entities; $i > 0; $i--) {
+			$entity = new ElggObject();
+			$entity->type = 'object';
+			$entity->subtype = 'test_5357_subtype';
+			$entity->access_id = ACCESS_PUBLIC;
+			$entity->save();
+			$guids[] = $entity->guid;
+			_elgg_invalidate_cache_for_entity($entity->guid);
+		}
+
+		// break entities such that the first fetch has one incomplete
+		// and the second and third fetches have only incompletes!
+		$db_prefix = elgg_get_config('dbprefix');
+		delete_data("
+			DELETE FROM {$db_prefix}objects_entity
+			WHERE guid IN ({$guids[1]}, {$guids[2]}, {$guids[3]}, {$guids[4]}, {$guids[5]})
+		");
+
+		$options = array(
+			'type' => 'object',
+			'subtype' => 'test_5357_subtype',
+			'order_by' => 'e.guid',
+		);
+
+		$entities_visited = array();
+		$batch = new ElggBatch('elgg_get_entities', $options, null, 2);
+		/* @var ElggEntity[] $batch */
+		foreach ($batch as $entity) {
+			$entities_visited[] = $entity->guid;
+		}
+
+		// The broken entities should not have been visited
+		$this->assertEqual($entities_visited, array($guids[0], $guids[6], $guids[7]));
+
+		// cleanup (including leftovers from previous tests)
+		$entity_rows = elgg_get_entities(array_merge($options, array(
+			'callback' => '',
+			'limit' => false,
+		)));
+		$guids = array();
+		foreach ($entity_rows as $row) {
+			$guids[] = $row->guid;
+		}
+		delete_data("DELETE FROM {$db_prefix}entities WHERE guid IN (" . implode(',', $guids) . ")");
+		delete_data("DELETE FROM {$db_prefix}objects_entity WHERE guid IN (" . implode(',', $guids) . ")");
+	}
+
+	public function testElggBatchDeleteHandlesBrokenEntities() {
+		$num_test_entities = 8;
+		$guids = array();
+		for ($i = $num_test_entities; $i > 0; $i--) {
+			$entity = new ElggObject();
+			$entity->type = 'object';
+			$entity->subtype = 'test_5357_subtype';
+			$entity->access_id = ACCESS_PUBLIC;
+			$entity->save();
+			$guids[] = $entity->guid;
+			_elgg_invalidate_cache_for_entity($entity->guid);
+		}
+
+		// break entities such that the first fetch has one incomplete
+		// and the second and third fetches have only incompletes!
+		$db_prefix = elgg_get_config('dbprefix');
+		delete_data("
+			DELETE FROM {$db_prefix}objects_entity
+			WHERE guid IN ({$guids[1]}, {$guids[2]}, {$guids[3]}, {$guids[4]}, {$guids[5]})
+		");
+
+		$options = array(
+			'type' => 'object',
+			'subtype' => 'test_5357_subtype',
+			'order_by' => 'e.guid',
+		);
+
+		$entities_visited = array();
+		$batch = new ElggBatch('elgg_get_entities', $options, null, 2, false);
+		/* @var ElggEntity[] $batch */
+		foreach ($batch as $entity) {
+			$entities_visited[] = $entity->guid;
+			$entity->delete();
+		}
+
+		// The broken entities should not have been visited
+		$this->assertEqual($entities_visited, array($guids[0], $guids[6], $guids[7]));
+
+		// cleanup (including leftovers from previous tests)
+		$entity_rows = elgg_get_entities(array_merge($options, array(
+			'callback' => '',
+			'limit' => false,
+		)));
+		$guids = array();
+		foreach ($entity_rows as $row) {
+			$guids[] = $row->guid;
+		}
+		delete_data("DELETE FROM {$db_prefix}entities WHERE guid IN (" . implode(',', $guids) . ")");
+		delete_data("DELETE FROM {$db_prefix}objects_entity WHERE guid IN (" . implode(',', $guids) . ")");
+	}
+
 	static function elgg_batch_callback_test($options, $reset = false) {
 		static $count = 1;
 
diff --git a/engine/tests/api/metadata.php b/engine/tests/api/metadata.php
index 825290d80..d23510c6a 100644
--- a/engine/tests/api/metadata.php
+++ b/engine/tests/api/metadata.php
@@ -123,9 +123,23 @@ class ElggCoreMetadataAPITest extends ElggCoreUnitTest {
 		$e->delete();
 	}
 
+	/**
+	 * https://github.com/Elgg/Elgg/issues/4867
+	 */
+	public function testElggGetEntityMetadataWhereSqlWithFalseValue() {
+		$pair = array('name' => 'test' , 'value' => false);
+		$result = elgg_get_entity_metadata_where_sql('e', 'metadata', null, null, $pair);
+		$where = preg_replace( '/\s+/', ' ', $result['wheres'][0]);
+		$this->assertTrue(strpos($where, "msn1.string = 'test' AND BINARY msv1.string = 0") > 0);
+
+		$result = elgg_get_entity_metadata_where_sql('e', 'metadata', array('test'), array(false));
+		$where = preg_replace( '/\s+/', ' ', $result['wheres'][0]);
+		$this->assertTrue(strpos($where, "msn.string IN ('test')) AND ( BINARY msv.string IN ('0')"));
+	}
+
 	// Make sure metadata with multiple values is correctly deleted when re-written
 	// by another user
-	// http://trac.elgg.org/ticket/2776
+	// https://github.com/elgg/elgg/issues/2776
 	public function test_elgg_metadata_multiple_values() {
 		$u1 = new ElggUser();
 		$u1->username = rand();
diff --git a/engine/tests/api/metadata_cache.php b/engine/tests/api/metadata_cache.php
index 846116a7b..7fb328169 100644
--- a/engine/tests/api/metadata_cache.php
+++ b/engine/tests/api/metadata_cache.php
@@ -166,4 +166,11 @@ class ElggCoreMetadataCacheTest extends ElggCoreUnitTest {
 		$actual = $this->cache->filterMetadataHeavyEntities($guids, 6000);
 		$this->assertIdentical($actual, $expected);
 	}
+
+	public function testCreateMetadataInvalidates() {
+		$this->obj1->foo = 1;
+		create_metadata($this->guid1, 'foo', 2, '', elgg_get_logged_in_user_guid(), ACCESS_FRIENDS);
+
+		$this->assertEqual($this->obj1->foo, 2);
+	}
 }
diff --git a/engine/tests/api/metastrings.php b/engine/tests/api/metastrings.php
index 0a8945084..5efdab972 100644
--- a/engine/tests/api/metastrings.php
+++ b/engine/tests/api/metastrings.php
@@ -55,8 +55,11 @@ class ElggCoreMetastringsTest extends ElggCoreUnitTest {
 	 * Called after each test method.
 	 */
 	public function tearDown() {
-		// do not allow SimpleTest to interpret Elgg notices as exceptions
-		$this->swallowErrors();
+		access_show_hidden_entities(true);
+		elgg_delete_annotations(array(
+			'guid' => $this->object->guid,
+		));
+		access_show_hidden_entities(false);
 	}
 
 	/**
@@ -98,6 +101,31 @@ class ElggCoreMetastringsTest extends ElggCoreUnitTest {
 		}
 	}
 
+	public function testGetMetastringObjectFromIDWithDisabledAnnotation() {
+		$name = 'test_annotation_name' . rand();
+		$value = 'test_annotation_value' . rand();
+		$id = create_annotation($this->object->guid, $name, $value);
+		$annotation = elgg_get_annotation_from_id($id);
+		$this->assertTrue($annotation->disable());
+
+		$test = elgg_get_metastring_based_object_from_id($id, 'annotation');
+		$this->assertEqual(false, $test);
+	}
+
+	public function testGetMetastringBasedObjectWithDisabledAnnotation() {
+		$name = 'test_annotation_name' . rand();
+		$value = 'test_annotation_value' . rand();
+		$id = create_annotation($this->object->guid, $name, $value);
+		$annotation = elgg_get_annotation_from_id($id);
+		$this->assertTrue($annotation->disable());
+
+		$test = elgg_get_metastring_based_objects(array(
+			'metastring_type' => 'annotations',
+			'guid' => $this->object->guid,
+		));
+		$this->assertEqual(array(), $test);
+	}
+
 	public function testEnableDisableByID() {
 		$db_prefix = elgg_get_config('dbprefix');
 		$annotations = $this->createAnnotations(1);
@@ -119,7 +147,6 @@ class ElggCoreMetastringsTest extends ElggCoreUnitTest {
 			// enable
 			$ashe = access_get_show_hidden_status();
 			access_show_hidden_entities(true);
-			flush();
 			$this->assertTrue(elgg_set_metastring_based_object_enabled_by_id($id, 'yes', $type));
 
 			$test = get_data($q);
diff --git a/engine/tests/api/plugins.php b/engine/tests/api/plugins.php
index 114f3991b..d0f111c48 100644
--- a/engine/tests/api/plugins.php
+++ b/engine/tests/api/plugins.php
@@ -69,7 +69,7 @@ class ElggCorePluginsAPITest extends ElggCoreUnitTest {
 			'description' => 'A longer, more interesting description.',
 			'website' => 'http://www.elgg.org/',
 			'repository' => 'https://github.com/Elgg/Elgg',
-			'bugtracker' => 'http://trac.elgg.org',
+			'bugtracker' => 'https://github.com/elgg/elgg/issues',
 			'donations' => 'http://elgg.org/supporter.php',
 			'copyright' => '(C) Elgg Foundation 2011',
 			'license' => 'GNU General Public License version 2',
@@ -174,7 +174,7 @@ class ElggCorePluginsAPITest extends ElggCoreUnitTest {
 	}
 	
 		public function testElggPluginManifestGetBugtracker() {
-		$this->assertEqual($this->manifest18->getBugTrackerURL(), 'http://trac.elgg.org');
+		$this->assertEqual($this->manifest18->getBugTrackerURL(), 'https://github.com/elgg/elgg/issues');
 		$this->assertEqual($this->manifest17->getBugTrackerURL(), '');
 	}
 	
diff --git a/engine/tests/objects/entities.php b/engine/tests/objects/entities.php
index 248b85c9e..bac72079e 100644
--- a/engine/tests/objects/entities.php
+++ b/engine/tests/objects/entities.php
@@ -271,7 +271,7 @@ class ElggCoreEntityTest extends ElggCoreUnitTest {
 		$this->save_entity();
 
 		// test deleting incorrectly
-		// @link http://trac.elgg.org/ticket/2273
+		// @link https://github.com/elgg/elgg/issues/2273
 		$this->assertNull($this->entity->deleteMetadata('impotent'));
 		$this->assertEqual($this->entity->important, 'indeed!');
 
diff --git a/engine/tests/objects/objects.php b/engine/tests/objects/objects.php
index 915594e0a..263ab2414 100644
--- a/engine/tests/objects/objects.php
+++ b/engine/tests/objects/objects.php
@@ -194,7 +194,7 @@ class ElggCoreObjectTest extends ElggCoreUnitTest {
 		$old = elgg_set_ignore_access(true);
 	}
 
-	// see http://trac.elgg.org/ticket/1196
+	// see https://github.com/elgg/elgg/issues/1196
 	public function testElggEntityRecursiveDisableWhenLoggedOut() {
 		$e1 = new ElggObject();
 		$e1->access_id = ACCESS_PUBLIC;
diff --git a/engine/tests/objects/users.php b/engine/tests/objects/users.php
index a3573acb6..8a1033ac4 100644
--- a/engine/tests/objects/users.php
+++ b/engine/tests/objects/users.php
@@ -65,6 +65,9 @@ class ElggCoreUserTest extends ElggCoreUnitTest {
 		$attributes['code'] = NULL;
 		$attributes['banned'] = 'no';
 		$attributes['admin'] = 'no';
+		$attributes['prev_last_action'] = NULL;
+		$attributes['last_login'] = NULL;
+		$attributes['prev_last_login'] = NULL;
 		ksort($attributes);
 
 		$entity_attributes = $this->user->expose_attributes();
@@ -142,7 +145,7 @@ class ElggCoreUserTest extends ElggCoreUnitTest {
 	}
 
 	public function testElggUserNameCache() {
-		// Trac #1305
+		// issue https://github.com/elgg/elgg/issues/1305
 
 		// very unlikely a user would have this username
 		$name = (string)time();
@@ -156,6 +159,22 @@ class ElggCoreUserTest extends ElggCoreUnitTest {
 		$this->assertFalse($user);
 	}
 
+	public function testGetUserByUsernameAcceptsUrlEncoded() {
+		$username = (string)time();
+		$this->user->username = $username;
+		$guid = $this->user->save();
+
+		// percent encode first letter
+		$first_letter = $username[0];
+		$first_letter = str_pad('%' . dechex(ord($first_letter)), 2, '0', STR_PAD_LEFT);
+		$username =   $first_letter . substr($username, 1);
+
+		$user = get_user_by_username($username);
+		$this->assertTrue((bool) $user);
+		$this->assertEqual($guid, $user->guid);
+
+		$this->user->delete();
+	}
 
 	public function testElggUserMakeAdmin() {
 		global $CONFIG;
diff --git a/engine/tests/regression/trac_bugs.php b/engine/tests/regression/trac_bugs.php
index 691433a41..689275661 100644
--- a/engine/tests/regression/trac_bugs.php
+++ b/engine/tests/regression/trac_bugs.php
@@ -1,7 +1,7 @@
 <?php
 /**
- * Elgg Regression Tests -- Trac Bugfixes
- * Any bugfixes from Trac that require testing belong here.
+ * Elgg Regression Tests -- GitHub Bugfixes
+ * Any bugfixes from GitHub that require testing belong here.
  *
  * @package Elgg
  * @subpackage Test
@@ -201,26 +201,28 @@ class ElggCoreRegressionBugsTest extends ElggCoreUnitTest {
 	}
 
 	/**
-	 * http://trac.elgg.org/ticket/3210 - Don't remove -s in friendly titles
-	 * http://trac.elgg.org/ticket/2276 - improve char encoding
+	 * https://github.com/elgg/elgg/issues/3210 - Don't remove -s in friendly titles
+	 * https://github.com/elgg/elgg/issues/2276 - improve char encoding
 	 */
 	public function test_friendly_title() {
 		$cases = array(
+			// acid test
+			"B&N > Amazon, OK? <bold> 'hey!' $34"
+			=> "bn-amazon-ok-bold-hey-34",
+
 			// hyphen, underscore and ASCII whitespace replaced by separator,
 			// other non-alphanumeric ASCII removed
-			"a-a_a a\na\ra\ta\va!a\"a#a\$a%a&a'a(a)a*a+a,a.a/a:a;a<a=a>a?a@a[a\\a]a^a`a{a|a}a~a"
-			=> "a-a-a-a-a-a-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
-
+			"a-a_a a\na\ra\ta\va!a\"a#a\$a%aa'a(a)a*a+a,a.a/a:a;a=a?a@a[a\\a]a^a`a{a|a}a~a"
+			=> "a-a-a-a-a-a-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaa",
+			
 			// separators trimmed
-			"-_ hello _-" => "hello",
+			"-_ hello _-"
+			=> "hello",
 
 			// accents removed, lower case, other multibyte chars are URL encoded
 			"I\xC3\xB1t\xC3\xABrn\xC3\xA2ti\xC3\xB4n\xC3\xA0liz\xC3\xA6ti\xC3\xB8n, AND \xE6\x97\xA5\xE6\x9C\xAC\xE8\xAA\x9E"
 				// Iñtërnâtiônàlizætiøn, AND 日本語
 			=> 'internationalizaetion-and-%E6%97%A5%E6%9C%AC%E8%AA%9E',
-
-			// some HTML entity replacements
-			"Me &amp; You" => 'me-and-you',
 		);
 
 		// where available, string is converted to NFC before transliteration
@@ -234,4 +236,170 @@ class ElggCoreRegressionBugsTest extends ElggCoreUnitTest {
 			$this->assertIdentical($expected, $friendly_title);
 		}
 	}
+
+	/**
+	 * Test #5369 -- parse_urls()
+	 * https://github.com/Elgg/Elgg/issues/5369
+	 */
+	public function test_parse_urls() {
+
+		$cases = array(
+			'no.link.here' =>
+				'no.link.here',
+			'simple link http://example.org test' =>
+				'simple link <a href="http://example.org" rel="nofollow">http:/<wbr />/<wbr />example.org</a> test',
+			'non-ascii http://ñew.org/ test' =>
+				'non-ascii <a href="http://ñew.org/" rel="nofollow">http:/<wbr />/<wbr />ñew.org/<wbr /></a> test',
+
+			// section 2.1
+			'percent encoded http://example.org/a%20b test' =>
+				'percent encoded <a href="http://example.org/a%20b" rel="nofollow">http:/<wbr />/<wbr />example.org/<wbr />a%20b</a> test',
+			// section 2.2: skipping single quote and parenthese
+			'reserved characters http://example.org/:/?#[]@!$&*+,;= test' =>
+				'reserved characters <a href="http://example.org/:/?#[]@!$&*+,;=" rel="nofollow">http:/<wbr />/<wbr />example.org/<wbr />:/<wbr />?#[]@!$&*+,;=</a> test',
+			// section 2.3
+			'unreserved characters http://example.org/a1-._~ test' =>
+				'unreserved characters <a href="http://example.org/a1-._~" rel="nofollow">http:/<wbr />/<wbr />example.org/<wbr />a1-._~</a> test',
+
+			'parameters http://example.org/?val[]=1&val[]=2 test' =>
+				'parameters <a href="http://example.org/?val[]=1&val[]=2" rel="nofollow">http:/<wbr />/<wbr />example.org/<wbr />?val[]=1&val[]=2</a> test',
+			'port http://example.org:80/ test' =>
+				'port <a href="http://example.org:80/" rel="nofollow">http:/<wbr />/<wbr />example.org:80/<wbr /></a> test',
+
+			'parentheses (http://www.google.com) test' =>
+				'parentheses (<a href="http://www.google.com" rel="nofollow">http:/<wbr />/<wbr />www.google.com</a>) test',
+			'comma http://elgg.org, test' =>
+				'comma <a href="http://elgg.org" rel="nofollow">http:/<wbr />/<wbr />elgg.org</a>, test',
+			'period http://elgg.org. test' =>
+				'period <a href="http://elgg.org" rel="nofollow">http:/<wbr />/<wbr />elgg.org</a>. test',
+			'exclamation http://elgg.org! test' =>
+				'exclamation <a href="http://elgg.org" rel="nofollow">http:/<wbr />/<wbr />elgg.org</a>! test',
+
+			'already anchor <a href="http://twitter.com/">twitter</a> test' =>
+				'already anchor <a href="http://twitter.com/">twitter</a> test',
+
+			'ssl https://example.org/ test' =>
+				'ssl <a href="https://example.org/" rel="nofollow">https:/<wbr />/<wbr />example.org/<wbr /></a> test',
+			'ftp ftp://example.org/ test' =>
+				'ftp <a href="ftp://example.org/" rel="nofollow">ftp:/<wbr />/<wbr />example.org/<wbr /></a> test',
+
+			'web archive anchor <a href="http://web.archive.org/web/20000229040250/http://www.google.com/">google</a>' =>
+				'web archive anchor <a href="http://web.archive.org/web/20000229040250/http://www.google.com/">google</a>',
+
+			'single quotes already anchor <a href=\'http://www.yahoo.com\'>yahoo</a>' =>
+				'single quotes already anchor <a href=\'http://www.yahoo.com\'>yahoo</a>',
+
+			'unquoted already anchor <a href=http://www.yahoo.com>yahoo</a>' =>
+				'unquoted already anchor <a href=http://www.yahoo.com>yahoo</a>',
+
+			'parens in uri http://thedailywtf.com/Articles/A-(Long-Overdue)-BuildMaster-Introduction.aspx' =>
+				'parens in uri <a href="http://thedailywtf.com/Articles/A-(Long-Overdue)-BuildMaster-Introduction.aspx" rel="nofollow">http:/<wbr />/<wbr />thedailywtf.com/<wbr />Articles/<wbr />A-(Long-Overdue)-BuildMaster-Introduction.aspx</a>'
+		);
+		foreach ($cases as $input => $output) {
+			$this->assertEqual($output, parse_urls($input));
+		}
+	}
+	
+	/**
+	 * Ensure additional select columns do not end up in entity attributes.
+	 *
+	 * https://github.com/Elgg/Elgg/issues/5538
+	 */
+	public function test_extra_columns_dont_appear_in_attributes() {
+		global $ENTITY_CACHE;
+
+		// may not have groups in DB - let's create one
+		$group = new ElggGroup();
+		$group->name = 'test_group';
+		$group->access_id = ACCESS_PUBLIC;
+		$this->assertTrue($group->save() !== false);
+		
+		// entity cache interferes with our test
+		$ENTITY_CACHE = array();
+		
+		foreach (array('site', 'user', 'group', 'object') as $type) {
+			$entities = elgg_get_entities(array(
+				'type' => $type,
+				'selects' => array('1 as _nonexistent_test_column'),
+				'limit' => 1,
+			));
+			if (!$this->assertTrue($entities, "Query for '$type' did not return an entity.")) {
+				continue;
+			}
+			$entity = $entities[0];
+			$this->assertNull($entity->_nonexistent_test_column, "Additional select columns are leaking to attributes for '$type'");
+		}
+		
+		$group->delete();
+	}
+
+	/**
+	 * Ensure that ElggBatch doesn't go into infinite loop when disabling annotations recursively when show hidden is enabled.
+	 *
+	 * https://github.com/Elgg/Elgg/issues/5952
+	 */
+	public function test_disabling_annotations_infinite_loop() {
+
+		//let's have some entity
+		$group = new ElggGroup();
+		$group->name = 'test_group';
+		$group->access_id = ACCESS_PUBLIC;
+		$this->assertTrue($group->save() !== false);
+
+		$total = 51;
+		//add some annotations
+		for ($cnt = 0; $cnt < $total; $cnt++) {
+			$group->annotate('test_annotation', 'value_' . $total);
+		}
+
+		//disable them
+		$show_hidden = access_get_show_hidden_status();
+		access_show_hidden_entities(true);
+		$options = array(
+			'guid' => $group->guid,
+			'limit' => $total, //using strict limit to avoid real infinite loop and just see ElggBatch limiting on it before finishing the work
+		);
+		elgg_disable_annotations($options);
+		access_show_hidden_entities($show_hidden);
+
+		//confirm all being disabled
+		$annotations = $group->getAnnotations(array(
+			'limit' => $total,
+		));
+		foreach ($annotations as $annotation) {
+			$this->assertTrue($annotation->enabled == 'no');
+		}
+
+		//delete group and annotations
+		$group->delete();
+	}
+
+	public function test_ElggXMLElement_does_not_load_external_entities() {
+		$elLast = libxml_disable_entity_loader(false);
+
+		// build payload that should trigger loading of external entity
+		$payload = file_get_contents(dirname(dirname(__FILE__)) . '/test_files/xxe/request.xml');
+		$path = realpath(dirname(dirname(__FILE__)) . '/test_files/xxe/external_entity.txt');
+		$path = str_replace('\\', '/', $path);
+		if ($path[0] != '/') {
+			$path = '/' . $path;
+		}
+		$path = 'file://' . $path;
+		$payload = sprintf($payload, $path);
+
+		// make sure we can actually this in this environment
+		$element = new SimpleXMLElement($payload);
+		$can_load_entity = preg_match('/secret/', (string)$element->methodName);
+
+		$this->skipUnless($can_load_entity, "XXE vulnerability cannot be tested on this system");
+
+		if ($can_load_entity) {
+			$el = new ElggXMLElement($payload);
+			$chidren = $el->getChildren();
+			$content = $chidren[0]->getContent();
+			$this->assertNoPattern('/secret/', $content);
+		}
+
+		libxml_disable_entity_loader($elLast);
+	}
 }
diff --git a/engine/tests/test_files/plugin_18/manifest.xml b/engine/tests/test_files/plugin_18/manifest.xml
index 5d788616a..c8b407511 100644
--- a/engine/tests/test_files/plugin_18/manifest.xml
+++ b/engine/tests/test_files/plugin_18/manifest.xml
@@ -7,7 +7,7 @@
 	<description>A longer, more interesting description.</description>
 	<website>http://www.elgg.org/</website>
 	<repository>https://github.com/Elgg/Elgg</repository>
-	<bugtracker>http://trac.elgg.org</bugtracker>
+	<bugtracker>https://github.com/elgg/elgg/issues</bugtracker>
 	<donations>http://elgg.org/supporter.php</donations>
 	<copyright>(C) Elgg Foundation 2011</copyright>
 	<license>GNU General Public License version 2</license>
diff --git a/engine/tests/test_files/xxe/external_entity.txt b/engine/tests/test_files/xxe/external_entity.txt
new file mode 100644
index 000000000..536aca34d
--- /dev/null
+++ b/engine/tests/test_files/xxe/external_entity.txt
@@ -0,0 +1 @@
+secret
\ No newline at end of file
diff --git a/engine/tests/test_files/xxe/request.xml b/engine/tests/test_files/xxe/request.xml
new file mode 100644
index 000000000..4390f9db2
--- /dev/null
+++ b/engine/tests/test_files/xxe/request.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<!DOCTYPE foo [
+<!ELEMENT methodName ANY >
+<!ENTITY xxe SYSTEM "%s" >
+]>
+<methodCall>
+    <methodName>test&xxe;test</methodName>
+</methodCall>