diff --git a/PHPCI/BuildFactory.php b/PHPCI/BuildFactory.php
index 77917c26..ad4dd0a5 100644
--- a/PHPCI/BuildFactory.php
+++ b/PHPCI/BuildFactory.php
@@ -20,6 +20,10 @@ use PHPCI\Model\Build\BitbucketBuild;
 */
 class BuildFactory
 {
+    /**
+    * Takes a generic build and returns a type-specific build model.
+    * @return PHPCI\Model\Build\LocalBuild|PHPCI\Model\Build\GithubBuild|PHPCI\Model\Build\BitbucketBuild
+    */
     public static function getBuild(Build $base)
     {
         switch($base->getProject()->getType())
diff --git a/PHPCI/Command/GenerateCommand.php b/PHPCI/Command/GenerateCommand.php
index c74d0632..35188c3c 100644
--- a/PHPCI/Command/GenerateCommand.php
+++ b/PHPCI/Command/GenerateCommand.php
@@ -30,6 +30,9 @@ class GenerateCommand extends Command
             ->setDescription('Generate models and stores from the database.');
     }
 
+    /**
+    * Generates Model and Store classes by reading database meta data.
+    */
     protected function execute()
     {
         $gen = new \b8\Database\CodeGenerator(\b8\Database::getConnection(), 'PHPCI', PHPCI_DIR . '/PHPCI/');
diff --git a/PHPCI/Command/InstallCommand.php b/PHPCI/Command/InstallCommand.php
index 93cfe25a..73d962c7 100644
--- a/PHPCI/Command/InstallCommand.php
+++ b/PHPCI/Command/InstallCommand.php
@@ -32,16 +32,21 @@ class InstallCommand extends Command
             ->setDescription('Install PHPCI.');
     }
 
+    /**
+    * Installs PHPCI - Can be run more than once as long as you ^C instead of entering an email address.
+    */
     protected function execute()
     {
+        // Gather initial data from the user:
         $dbHost = $this->ask('Enter your MySQL host: ');
         $dbName = $this->ask('Enter the database name PHPCI should use: ');
         $dbUser = $this->ask('Enter your MySQL username: ');
         $dbPass = $this->ask('Enter your MySQL password: ', true);
-        $ciUrl = $this->ask('Your PHPCI URL (without trailing slash): ', true);
+        $ciUrl = $this->ask('Your PHPCI URL (without trailing slash): ');
         $ghId = $this->ask('(Optional) Github Application ID: ', true);
         $ghSecret = $this->ask('(Optional) Github Application Secret: ', true);
 
+        // Create the database if it doesn't exist:
         $cmd    = 'mysql -u' . $dbUser . (!empty($dbPass) ? ' -p' . $dbPass : '') . ' -h' . $dbHost .
                     ' -e "CREATE DATABASE IF NOT EXISTS ' . $dbName . '"';
 
@@ -61,21 +66,28 @@ b8\Database::setReadServers(array('{$dbHost}'));
 \$registry->set('install_url', '{$ciUrl}');
 ";
 
+        // Has the user entered Github app details? If so add those to config:
         if (!empty($ghId) && !empty($ghSecret)) {
             $str .= PHP_EOL .
                     "\$registry->set('github_app', array('id' => '{$ghId}', 'secret' => '{$ghSecret}'));" .
                     PHP_EOL;
         }
 
-
+        // Write the config file and then re-bootstrap:
         file_put_contents(PHPCI_DIR . 'config.php', $str);
-
         require(PHPCI_DIR . 'bootstrap.php');
 
+        // Update the database:
         $gen = new \b8\Database\Generator(\b8\Database::getConnection(), 'PHPCI', './PHPCI/Model/Base/');
         $gen->generate();
 
-        $adminEmail = $this->ask('Enter your email address: ');
+        // Try to create a user account:
+        $adminEmail = $this->ask('Enter your email address (leave blank if updating): ', true);
+
+        if (empty($adminEmail)) {
+            return;
+        }
+        
         $adminPass = $this->ask('Enter your desired admin password: ');
         $adminName = $this->ask('Enter your name: ');
 
diff --git a/PHPCI/Command/RunCommand.php b/PHPCI/Command/RunCommand.php
index 5d776f9b..b28d9832 100644
--- a/PHPCI/Command/RunCommand.php
+++ b/PHPCI/Command/RunCommand.php
@@ -33,6 +33,9 @@ class RunCommand extends Command
             ->setDescription('Run all pending PHPCI builds.');
     }
 
+    /**
+    * Pulls all pending builds from the database and runs them.
+    */
     protected function execute(InputInterface $input, OutputInterface $output)
     {
         $this->output = $output;
@@ -53,6 +56,10 @@ class RunCommand extends Command
         }
     }
 
+    /**
+    * Called when log entries are made in Builder / the plugins.
+    * @see \PHPCI\Builder::log()
+    */
     public function logCallback($log)
     {
         $this->output->writeln($log);
diff --git a/PHPCI/Controller/BitbucketController.php b/PHPCI/Controller/BitbucketController.php
index 3ca3421b..b0011336 100644
--- a/PHPCI/Controller/BitbucketController.php
+++ b/PHPCI/Controller/BitbucketController.php
@@ -26,6 +26,9 @@ class BitbucketController extends b8\Controller
         $this->_buildStore      = Store\Factory::getStore('Build');
     }
 
+    /**
+    * Called by Bitbucket POST service.
+    */
     public function webhook($project)
     {
         $payload    = json_decode($this->getParam('payload'), true);
diff --git a/PHPCI/Controller/BuildController.php b/PHPCI/Controller/BuildController.php
index d7c90b49..c590f4f8 100644
--- a/PHPCI/Controller/BuildController.php
+++ b/PHPCI/Controller/BuildController.php
@@ -26,6 +26,9 @@ class BuildController extends b8\Controller
         $this->_buildStore      = b8\Store\Factory::getStore('Build');
     }
 
+    /**
+    * View a specific build.
+    */
     public function view($buildId)
     {
         $build          = $this->_buildStore->getById($buildId);
@@ -37,11 +40,17 @@ class BuildController extends b8\Controller
         return $view->render();
     }
 
+    /**
+    * AJAX call to get build data:
+    */
     public function data($buildId)
     {
         die($this->getBuildData($buildId));
     }
 
+    /**
+    * Get build data from database and json encode it:
+    */
     protected function getBuildData($buildId)
     {
         $build  = $this->_buildStore->getById($buildId);
@@ -57,6 +66,9 @@ class BuildController extends b8\Controller
         return json_encode($data);
     }
 
+    /**
+    * Create a build using an existing build as a template:
+    */
     public function rebuild($buildId)
     {
         $copy   = $this->_buildStore->getById($buildId);
@@ -73,6 +85,9 @@ class BuildController extends b8\Controller
         header('Location: /build/view/' . $build->getId());
     }
 
+    /**
+    * Delete a build.
+    */
     public function delete($buildId)
     {
         if (!Registry::getInstance()->get('user')->getIsAdmin()) {
@@ -85,6 +100,9 @@ class BuildController extends b8\Controller
         header('Location: /project/view/' . $build->getProjectId());
     }
 
+    /**
+    * Parse log for unix colours and replace with HTML.
+    */
     protected function cleanLog($log)
     {
         $log = str_replace('[0;32m', '<span style="color: green">', $log);
diff --git a/PHPCI/Controller/GithubController.php b/PHPCI/Controller/GithubController.php
index fccac1c5..a2a92e68 100644
--- a/PHPCI/Controller/GithubController.php
+++ b/PHPCI/Controller/GithubController.php
@@ -26,6 +26,9 @@ class GithubController extends b8\Controller
         $this->_buildStore      = Store\Factory::getStore('Build');
     }
 
+    /**
+    * Called by Github Webhooks:
+    */
     public function webhook($project)
     {
         $payload    = json_decode($this->getParam('payload'), true);
diff --git a/PHPCI/Controller/IndexController.php b/PHPCI/Controller/IndexController.php
index 1c03c803..2633ab87 100644
--- a/PHPCI/Controller/IndexController.php
+++ b/PHPCI/Controller/IndexController.php
@@ -25,6 +25,9 @@ class IndexController extends b8\Controller
         $this->_projectStore    = b8\Store\Factory::getStore('Project');
     }
 
+    /**
+    * Display PHPCI dashboard:
+    */
     public function index()
     {
         $projects       = $this->_projectStore->getWhere(array(), 50, 0, array(), array('title' => 'ASC'));
@@ -35,11 +38,17 @@ class IndexController extends b8\Controller
         return $view->render();
     }
 
+    /**
+    * AJAX get latest builds table (HTML)
+    */
     public function latest()
     {
         die($this->getLatestBuildsHtml());
     }
 
+    /**
+    * Get latest builds and render as a table.
+    */
     protected function getLatestBuildsHtml()
     {
         $builds         = $this->_buildStore->getWhere(array(), 10, 0, array(), array('id' => 'DESC'));
diff --git a/PHPCI/Controller/ProjectController.php b/PHPCI/Controller/ProjectController.php
index 54c6e28c..092b1276 100644
--- a/PHPCI/Controller/ProjectController.php
+++ b/PHPCI/Controller/ProjectController.php
@@ -29,6 +29,9 @@ class ProjectController extends b8\Controller
         $this->_projectStore    = b8\Store\Factory::getStore('Project');
     }
 
+    /**
+    * View a specific project.
+    */
     public function view($projectId)
     {
         $project        = $this->_projectStore->getById($projectId);
@@ -44,6 +47,9 @@ class ProjectController extends b8\Controller
         return $view->render();
     }
 
+    /**
+    * Create a new pending build for a project.
+    */
     public function build($projectId)
     {
         $build = new Build();
@@ -58,6 +64,9 @@ class ProjectController extends b8\Controller
         header('Location: /build/view/' . $build->getId());
     }
 
+    /**
+    * Delete a project.
+    */
     public function delete($projectId)
     {
         if (!Registry::getInstance()->get('user')->getIsAdmin()) {
@@ -70,12 +79,18 @@ class ProjectController extends b8\Controller
         header('Location: /');
     }
 
+    /**
+    * AJAX get latest builds.
+    */
     public function builds($projectId)
     {
         $builds = $this->getLatestBuildsHtml($projectId);
         die($builds[0]);
     }
 
+    /**
+    * Render latest builds for project as HTML table.
+    */
     protected function getLatestBuildsHtml($projectId, $start = 0)
     {
         $criteria       = array('project_id' => $projectId);
@@ -87,6 +102,9 @@ class ProjectController extends b8\Controller
         return array($view->render(), $builds['count']);
     }
 
+    /**
+    * Add a new project. Handles both the form, and processing.
+    */
     public function add()
     {
         if (!Registry::getInstance()->get('user')->getIsAdmin()) {
@@ -150,6 +168,9 @@ class ProjectController extends b8\Controller
         die;
     }
 
+    /**
+    * Handles log in with Github
+    */
     protected function handleGithubResponse()
     {
         $github     = \b8\Registry::getInstance()->get('github_app');
@@ -170,6 +191,9 @@ class ProjectController extends b8\Controller
         }
     }
 
+    /**
+    * Edit a project. Handles both the form and processing. 
+    */
     public function edit($projectId)
     {
         if (!Registry::getInstance()->get('user')->getIsAdmin()) {
@@ -208,6 +232,9 @@ class ProjectController extends b8\Controller
         die;
     }
 
+    /**
+    * Create add / edit project form. 
+    */
     protected function projectForm($values, $type = 'add')
     {
         $form = new Form();
@@ -289,6 +316,9 @@ class ProjectController extends b8\Controller
         return $form;
     }
 
+    /**
+    * Get an array of repositories from Github's API.
+    */
     protected function getGithubRepositories()
     {
         $http = new \b8\HttpClient();
diff --git a/PHPCI/Controller/SessionController.php b/PHPCI/Controller/SessionController.php
index 9d52d788..7e806a21 100644
--- a/PHPCI/Controller/SessionController.php
+++ b/PHPCI/Controller/SessionController.php
@@ -24,6 +24,9 @@ class SessionController extends b8\Controller
         $this->_userStore       = b8\Store\Factory::getStore('User');
     }
 
+    /**
+    * Handles user login (form and processing)
+    */
     public function login()
     {
         if (b8\Registry::getInstance()->get('requestMethod') == 'POST') {
@@ -62,6 +65,9 @@ class SessionController extends b8\Controller
         die($view->render());
     }
 
+    /**
+    * Handles user logout.
+    */
     public function logout()
     {
         unset($_SESSION['user_id']);
diff --git a/PHPCI/Controller/UserController.php b/PHPCI/Controller/UserController.php
index 39857aab..dc77ff0a 100644
--- a/PHPCI/Controller/UserController.php
+++ b/PHPCI/Controller/UserController.php
@@ -27,6 +27,9 @@ class UserController extends b8\Controller
         $this->_userStore       = b8\Store\Factory::getStore('User');
     }
 
+    /**
+    * View user list.
+    */
     public function index()
     {
         $users          = $this->_userStore->getWhere(array(), 1000, 0, array(), array('email' => 'ASC'));
@@ -36,6 +39,9 @@ class UserController extends b8\Controller
         return $view->render();
     }
 
+    /**
+    * Add a user - handles both form and processing.
+    */
     public function add()
     {
         if (!Registry::getInstance()->get('user')->getIsAdmin()) {
@@ -74,6 +80,9 @@ class UserController extends b8\Controller
         die;
     }
 
+    /**
+    * Edit a user - handles both form and processing.
+    */
     public function edit($userId)
     {
         if (!Registry::getInstance()->get('user')->getIsAdmin()) {
@@ -115,6 +124,9 @@ class UserController extends b8\Controller
         die;
     }
 
+    /**
+    * Create user add / edit form.
+    */
     protected function userForm($values, $type = 'add')
     {
         $form = new Form();
@@ -155,6 +167,9 @@ class UserController extends b8\Controller
         return $form;
     }
 
+    /**
+    * Delete a user.
+    */
     public function delete($userId)
     {
         if (!Registry::getInstance()->get('user')->getIsAdmin()) {
diff --git a/PHPCI/Model/Build.php b/PHPCI/Model/Build.php
index 5230b42c..e60ff64e 100644
--- a/PHPCI/Model/Build.php
+++ b/PHPCI/Model/Build.php
@@ -21,21 +21,33 @@ use PHPCI\Builder;
 */
 class Build extends BuildBase
 {
+    /**
+    * Get link to commit from another source (i.e. Github)
+    */
     public function getCommitLink()
     {
         return '#';
     }
 
+    /**
+    * Get link to branch from another source (i.e. Github)
+    */
     public function getBranchLink()
     {
         return '#';
     }
 
+    /**
+    * Send status updates to any relevant third parties (i.e. Github)
+    */
     public function sendStatusPostback()
     {
         return;
     }
 
+    /**
+    * Create a working copy by cloning, copying, or similar.
+    */
     public function createWorkingCopy(Builder $builder, $buildPath)
     {
     }
diff --git a/PHPCI/Model/Build/BitbucketBuild.php b/PHPCI/Model/Build/BitbucketBuild.php
index 485c66e8..fb50a710 100644
--- a/PHPCI/Model/Build/BitbucketBuild.php
+++ b/PHPCI/Model/Build/BitbucketBuild.php
@@ -20,16 +20,25 @@ use PHPCI\Model\Build\RemoteGitBuild;
 */
 class BitbucketBuild extends RemoteGitBuild
 {
+    /**
+    * Get link to commit from another source (i.e. Github)
+    */
     public function getCommitLink()
     {
         return 'https://bitbucket.org/' . $this->getProject()->getReference() . '/commits/' . $this->getCommitId();
     }
 
+    /**
+    * Get link to branch from another source (i.e. Github)
+    */
     public function getBranchLink()
     {
         return 'https://bitbucket.org/' . $this->getProject()->getReference() . '/src/?at=' . $this->getBranch();
     }
 
+    /**
+    * Get the URL to be used to clone this remote repository.
+    */
     protected function getCloneUrl()
     {
         $key = trim($this->getProject()->getGitKey());
diff --git a/PHPCI/Model/Build/GithubBuild.php b/PHPCI/Model/Build/GithubBuild.php
index e08e31f4..35ce439b 100644
--- a/PHPCI/Model/Build/GithubBuild.php
+++ b/PHPCI/Model/Build/GithubBuild.php
@@ -19,16 +19,25 @@ use PHPCI\Model\Build\RemoteGitBuild;
 */
 class GithubBuild extends RemoteGitBuild
 {
+    /**
+    * Get link to commit from another source (i.e. Github)
+    */
     public function getCommitLink()
     {
         return 'https://github.com/' . $this->getProject()->getReference() . '/commit/' . $this->getCommitId();
     }
 
+    /**
+    * Get link to branch from another source (i.e. Github)
+    */
     public function getBranchLink()
     {
         return 'https://github.com/' . $this->getProject()->getReference() . '/tree/' . $this->getBranch();
     }
 
+    /**
+    * Send status updates to any relevant third parties (i.e. Github)
+    */
     public function sendStatusPostback()
     {
         $project    = $this->getProject();
@@ -70,6 +79,9 @@ class GithubBuild extends RemoteGitBuild
         $http->request('POST', $url, json_encode($params));
     }
 
+    /**
+    * Get the URL to be used to clone this remote repository.
+    */
     protected function getCloneUrl()
     {
         $key = trim($this->getProject()->getGitKey());
diff --git a/PHPCI/Model/Build/LocalBuild.php b/PHPCI/Model/Build/LocalBuild.php
index 51c25145..38e2a914 100644
--- a/PHPCI/Model/Build/LocalBuild.php
+++ b/PHPCI/Model/Build/LocalBuild.php
@@ -21,6 +21,9 @@ use Symfony\Component\Yaml\Parser as YamlParser;
 */
 class LocalBuild extends Build
 {
+    /**
+    * Create a working copy by cloning, copying, or similar.
+    */
     public function createWorkingCopy(Builder $builder, $buildPath)
     {
         $reference  = $this->getProject()->getReference();
diff --git a/PHPCI/Model/Build/RemoteGitBuild.php b/PHPCI/Model/Build/RemoteGitBuild.php
index aafb4c8a..0ec2fc9f 100644
--- a/PHPCI/Model/Build/RemoteGitBuild.php
+++ b/PHPCI/Model/Build/RemoteGitBuild.php
@@ -21,8 +21,14 @@ use Symfony\Component\Yaml\Parser as YamlParser;
 */
 abstract class RemoteGitBuild extends Build
 {
+    /**
+    * Get the URL to be used to clone this remote repository.
+    */
     abstract protected function getCloneUrl();
 
+    /**
+    * Create a working copy by cloning, copying, or similar.
+    */
     public function createWorkingCopy(Builder $builder, $buildPath)
     {
         $yamlParser = new YamlParser();
@@ -51,11 +57,17 @@ abstract class RemoteGitBuild extends Build
         return true;
     }
 
+    /**
+    * Use an HTTP-based git clone.
+    */
     protected function cloneByHttp(Builder $builder, $to)
     {
         return $builder->executeCommand('git clone -b %s %s "%s"', $this->getBranch(), $this->getCloneUrl(), $to);
     }
 
+    /**
+    * Use an SSH-based git clone.
+    */
     protected function cloneBySsh(Builder $builder, $to)
     {
         // Copy the project's keyfile to disk:
diff --git a/PHPCI/Plugin/Composer.php b/PHPCI/Plugin/Composer.php
index 35e71be2..42195f52 100644
--- a/PHPCI/Plugin/Composer.php
+++ b/PHPCI/Plugin/Composer.php
@@ -29,6 +29,9 @@ class Composer implements \PHPCI\Plugin
         $this->action       = isset($options['action']) ? $options['action'] : 'update';
     }
 
+    /**
+    * Executes Composer and runs a specified command (e.g. install / update)
+    */
     public function execute()
     {
         $cmd = PHPCI_DIR . 'composer.phar --prefer-dist --working-dir="%s" %s';
diff --git a/PHPCI/Plugin/Mysql.php b/PHPCI/Plugin/Mysql.php
index 500dc922..a8d377b8 100644
--- a/PHPCI/Plugin/Mysql.php
+++ b/PHPCI/Plugin/Mysql.php
@@ -46,6 +46,9 @@ class Mysql implements \PHPCI\Plugin
         }
     }
 
+    /**
+    * Connects to MySQL and runs a specified set of queries.
+    */
     public function execute()
     {
         try {
diff --git a/PHPCI/Plugin/Pgsql.php b/PHPCI/Plugin/Pgsql.php
index 635753c2..e746dd72 100644
--- a/PHPCI/Plugin/Pgsql.php
+++ b/PHPCI/Plugin/Pgsql.php
@@ -41,6 +41,9 @@ class Pgsql implements \PHPCI\Plugin
         }
     }
 
+    /**
+    * Connects to PgSQL and runs a specified set of queries.
+    */
     public function execute()
     {
         try {
diff --git a/PHPCI/Plugin/PhpCodeSniffer.php b/PHPCI/Plugin/PhpCodeSniffer.php
index 13d915c8..4c3c2680 100644
--- a/PHPCI/Plugin/PhpCodeSniffer.php
+++ b/PHPCI/Plugin/PhpCodeSniffer.php
@@ -28,10 +28,13 @@ class PhpCodeSniffer implements \PHPCI\Plugin
         $this->standard     = isset($options['standard']) ? $options['standard'] : 'PSR2';
     }
 
+    /**
+    * Runs PHP Code Sniffer in a specified directory, to a specified standard.
+    */
     public function execute()
     {
         $ignore = '';
-                
+
         if (count($this->phpci->ignore)) {
             $ignore = ' --ignore=' . implode(',', $this->phpci->ignore);
         }
diff --git a/PHPCI/Plugin/PhpCpd.php b/PHPCI/Plugin/PhpCpd.php
index 1896d12f..5ec0bd9f 100644
--- a/PHPCI/Plugin/PhpCpd.php
+++ b/PHPCI/Plugin/PhpCpd.php
@@ -28,6 +28,9 @@ class PhpCpd implements \PHPCI\Plugin
         $this->standard     = isset($options['standard']) ? $options['standard'] : 'PSR2';
     }
 
+    /**
+    * Runs PHP Copy/Paste Detector in a specified directory.
+    */
     public function execute()
     {
         $ignore = '';
diff --git a/PHPCI/Plugin/PhpMessDetector.php b/PHPCI/Plugin/PhpMessDetector.php
index 42c59b08..ea6ff959 100644
--- a/PHPCI/Plugin/PhpMessDetector.php
+++ b/PHPCI/Plugin/PhpMessDetector.php
@@ -24,6 +24,9 @@ class PhpMessDetector implements \PHPCI\Plugin
         $this->phpci        = $phpci;
     }
 
+    /**
+    * Runs PHP Mess Detector in a specified directory.
+    */
     public function execute()
     {
         $ignore = '';
diff --git a/PHPCI/Plugin/PhpSpec.php b/PHPCI/Plugin/PhpSpec.php
index b6b11214..ace3f352 100644
--- a/PHPCI/Plugin/PhpSpec.php
+++ b/PHPCI/Plugin/PhpSpec.php
@@ -24,6 +24,9 @@ class PhpSpec implements \PHPCI\Plugin
         $this->phpci        = $phpci;
     }
 
+    /**
+    * Runs PHP Spec tests.
+    */
     public function execute()
     {
         $curdir = getcwd();
diff --git a/PHPCI/Plugin/PhpUnit.php b/PHPCI/Plugin/PhpUnit.php
index 71954839..c3fdb0a2 100644
--- a/PHPCI/Plugin/PhpUnit.php
+++ b/PHPCI/Plugin/PhpUnit.php
@@ -39,23 +39,26 @@ class PhpUnit implements \PHPCI\Plugin
     {
         $this->phpci        = $phpci;
 
-        if(isset($options['directory'])) {
+        if (isset($options['directory'])) {
             $this->directory = $options['directory'];
         }
 
-        if(isset($options['config'])) {
+        if (isset($options['config'])) {
             $this->xmlConfigFile = $options['config'];
         }
 
-        if(isset($options['run_from'])) {
+        if (isset($options['run_from'])) {
             $this->runFrom = $options['run_from'];
         }
 
-        if(isset($options['args'])) {
+        if (isset($options['args'])) {
             $this->args = $options['args'];
         }
     }
 
+    /**
+    * Runs PHP Unit tests in a specified directory, optionally using specified config file(s).
+    */
     public function execute()
     {
         $success = true;