diff --git a/config/packages/framework.yaml b/config/packages/framework.yaml
index b32f52d989..a31bc82c6a 100644
--- a/config/packages/framework.yaml
+++ b/config/packages/framework.yaml
@@ -1,15 +1,9 @@
 framework:
     secret: '%env(APP_SECRET)%'
-    #default_locale: en
-    #csrf_protection: ~
-    #http_method_override: true
 
-    # uncomment this entire section to enable sessions
-    #session:
-    #    # With this config, PHP's native session handling is used
-    #    handler_id: ~
+    # needs to be disabled because we currently use a different translator with the same service name
+    translator:
+        enabled: false
 
-    #esi: ~
-    #fragments: ~
     php_errors:
         log: true
diff --git a/src/phpDocumentor/Application.php b/src/phpDocumentor/Application.php
index da4ac12fa3..2ac1739c1f 100644
--- a/src/phpDocumentor/Application.php
+++ b/src/phpDocumentor/Application.php
@@ -64,26 +64,6 @@ public function __construct(ContainerInterface $container)
         $this->container = $container;
     }
 
-    /**
-     * @param null|InputInterface $input
-     * @param null|OutputInterface $output
-     * @return mixed
-     */
-    public function run(InputInterface $input = null, OutputInterface $output = null)
-    {
-        /** @var ConsoleApplication $app */
-        $app = $this['console'];
-        $app->setAutoExit(false);
-
-        if ($output === null) {
-            $output = new Console\Output\Output();
-            $output->setLogger($this['monolog']);
-        }
-
-        return parent::run(new ArgvInput(), $output);
-    }
-
-
     /**
      * Adjust php.ini settings.
      *
diff --git a/src/phpDocumentor/Application/CilexCompatibilityLayer/CilexCompatibilityLayerBundle.php b/src/phpDocumentor/Application/CilexCompatibilityLayer/CilexCompatibilityLayerBundle.php
index 537b72d533..2812980c7c 100644
--- a/src/phpDocumentor/Application/CilexCompatibilityLayer/CilexCompatibilityLayerBundle.php
+++ b/src/phpDocumentor/Application/CilexCompatibilityLayer/CilexCompatibilityLayerBundle.php
@@ -5,6 +5,10 @@
 namespace phpDocumentor\Application\CilexCompatibilityLayer;
 
 use phpDocumentor\Application;
+use phpDocumentor\Command\Helper\ConfigurationHelper;
+use phpDocumentor\Command\Helper\LoggerHelper;
+use phpDocumentor\Configuration;
+use Symfony\Component\Console\Input\InputOption;
 use Symfony\Component\HttpKernel\Bundle\Bundle;
 
 final class CilexCompatibilityLayerBundle extends Bundle
@@ -18,6 +22,21 @@ public function boot()
 
     public function registerCommands(\Symfony\Component\Console\Application $application)
     {
+        $application->getHelperSet()->set(new LoggerHelper());
+        $application->getHelperSet()->set(new ConfigurationHelper(new Configuration()));
+
+        $application->getDefinition()->addOption(
+            new InputOption(
+                'config',
+                'c',
+                InputOption::VALUE_OPTIONAL,
+                'Location of a custom configuration file'
+            )
+        );
+        $application->getDefinition()->addOption(
+            new InputOption('log', null, InputOption::VALUE_OPTIONAL, 'Log file to write to')
+        );
+
         if ($this->container->has('phpdocumentor.compatibility.extra_commands')) {
             $commands = $this->container->get('phpdocumentor.compatibility.extra_commands');
 
diff --git a/src/phpDocumentor/Command/Command.php b/src/phpDocumentor/Command/Command.php
index 6f4a7cc9ec..3988daccce 100644
--- a/src/phpDocumentor/Command/Command.php
+++ b/src/phpDocumentor/Command/Command.php
@@ -16,6 +16,7 @@
 use Symfony\Component\Console\Helper\HelperSet;
 use Symfony\Component\Console\Helper\ProgressHelper;
 use Symfony\Component\Console\Input\InputInterface;
+use Symfony\Component\Console\Output\OutputInterface;
 
 /**
  * Base command for phpDocumentor commands.
@@ -42,6 +43,24 @@ public function getService(string $name)
         return $this->getContainer()->get($name);
     }
 
+    /**
+     * Executes a callable piece of code and writes an entry to the log detailing how long it took.
+     */
+    protected function writeTimedLog(OutputInterface $output, $message, $operation, array $arguments = array())
+    {
+        $output->write(sprintf('%-66.66s .. ', $message));
+        $timerStart = microtime(true);
+
+        call_user_func_array($operation, $arguments);
+
+        $output->writeln(sprintf('%8.3fs', microtime(true) - $timerStart));
+    }
+
+    public function getService(string $name)
+    {
+        return $this->getContainer()->get($name);
+    }
+
     /**
      * Returns the Progress bar helper.
      *
diff --git a/src/phpDocumentor/Configuration/Loader.php b/src/phpDocumentor/Configuration/Loader.php
index c98bc9fa7d..3f2d33c906 100644
--- a/src/phpDocumentor/Configuration/Loader.php
+++ b/src/phpDocumentor/Configuration/Loader.php
@@ -12,7 +12,7 @@
 namespace phpDocumentor\Configuration;
 
 use JMS\Serializer\Serializer;
-use phpDocumentor\Console\Input\ArgvInput;
+use Symfony\Component\Console\Input\ArgvInput;
 
 /**
  * Loads the template and user-defined configuration file from disk and creates a Configuration object from it.
diff --git a/src/phpDocumentor/Configuration/ServiceProvider.php b/src/phpDocumentor/Configuration/ServiceProvider.php
index c6535db6d6..8cf03983b9 100644
--- a/src/phpDocumentor/Configuration/ServiceProvider.php
+++ b/src/phpDocumentor/Configuration/ServiceProvider.php
@@ -53,47 +53,15 @@ class ServiceProvider implements ServiceProviderInterface
      */
     public function register(Container $app)
     {
-        $this->addMerger($app);
-
-//        $app->extend(
-//            'console',
-//            function (ConsoleApplication $console) {
-//                $console->getDefinition()->addOption(
-//                    new InputOption(
-//                        'config',
-//                        'c',
-//                        InputOption::VALUE_OPTIONAL,
-//                        'Location of a custom configuration file'
-//                    )
-//                );
-//
-//                return $console;
-//            }
-//        );
-
         $app['config.path.template'] = __DIR__ . '/Resources/phpdoc.tpl.xml';
         $app['config.path.user'] = getcwd()
             . ((file_exists(getcwd() . '/phpdoc.xml')) ? '/phpdoc.xml' : '/phpdoc.dist.xml');
         $app['config.class'] = 'phpDocumentor\Configuration';
 
         $app['config'] = function ($app) {
-            $loader = new Loader($app['serializer'], $app['config.merger']);
+            $loader = new Loader($app['serializer'], new Merger(new AnnotationReader()));
 
             return $loader->load($app['config.path.template'], $app['config.path.user'], $app['config.class']);
         };
     }
-
-    /**
-     * Initializes and adds the configuration merger object as the 'config.merger' service to the container.
-     *
-     * @param Application $container
-     *
-     * @return void
-     */
-    private function addMerger(Application $container)
-    {
-        $container['config.merger'] = function () {
-            return new Merger(new AnnotationReader());
-        };
-    }
 }
diff --git a/src/phpDocumentor/Console/Input/ArgvInput.php b/src/phpDocumentor/Console/Input/ArgvInput.php
deleted file mode 100644
index 332fd3e9ed..0000000000
--- a/src/phpDocumentor/Console/Input/ArgvInput.php
+++ /dev/null
@@ -1,53 +0,0 @@
-<?php
-/**
- * phpDocumentor
- *
- * PHP Version 5.3
- *
- * @copyright 2010-2018 Mike van Riel / Naenius (http://www.naenius.com)
- * @license   http://www.opensource.org/licenses/mit-license.php MIT
- * @link      http://phpdoc.org
- */
-
-namespace phpDocumentor\Console\Input;
-
-use Symfony\Component\Console\Input\InputDefinition;
-
-/**
- * Argv input for the Console component of Symfony adapted to phpDocumentor.
- *
- * This InputStream for the Symfony Console component prepends the namespace and command
- * name `project:run` to the Argv array if no command has been provided.
- */
-class ArgvInput extends \Symfony\Component\Console\Input\ArgvInput
-{
-    /**
-     * Constructor.
-     *
-     * The constructor has been overridden to check whether the first element in
-     * the argument list is an argument (as it represents the command name).
-     *
-     * If it is not then we insert the command name: *project:run*.
-     *
-     * This way we can ensure that if no command name is given that the project
-     * defaults to the execution of phpDocumentor. This is behavior that is
-     * expected from previous releases of phpDocumentor.
-     *
-     * @param string[]        $argv       An array of parameters from the CLI (in the argv format)
-     * @param InputDefinition $definition A InputDefinition instance
-     *
-     * @api
-     */
-    public function __construct(array $argv = null, InputDefinition $definition = null)
-    {
-        if (null === $argv) {
-            $argv = $_SERVER['argv'];
-        }
-
-        if ((count($argv) === 1) || ($argv[1][0] === '-')) {
-            array_splice($argv, 1, 0, 'project:run');
-        }
-
-        parent::__construct($argv, $definition);
-    }
-}
diff --git a/src/phpDocumentor/Console/Output/Output.php b/src/phpDocumentor/Console/Output/Output.php
deleted file mode 100644
index b1fd0415a4..0000000000
--- a/src/phpDocumentor/Console/Output/Output.php
+++ /dev/null
@@ -1,85 +0,0 @@
-<?php
-/**
- * phpDocumentor
- *
- * PHP Version 5.3
- *
- * @copyright 2010-2018 Mike van Riel / Naenius (http://www.naenius.com)
- * @license   http://www.opensource.org/licenses/mit-license.php MIT
- * @link      http://phpdoc.org
- */
-
-namespace phpDocumentor\Console\Output;
-
-use Monolog\Logger;
-use Symfony\Component\Console\Output\ConsoleOutput;
-
-/**
- * A custom output class for our Console object that supports writing to the log.
- */
-class Output extends ConsoleOutput
-{
-    /** @var Logger Object used to log system and debug messages to. */
-    protected $logger;
-
-    /**
-     * Sets a logger object to write information to.
-     *
-     * @param Logger $logger
-     */
-    public function setLogger(Logger $logger)
-    {
-        $this->logger = $logger;
-    }
-
-    /**
-     * Returns the object where is being logged to.
-     *
-     * @return Logger
-     */
-    public function getLogger()
-    {
-        return $this->logger;
-    }
-
-    /**
-     * Executes a callable piece of code and writes an entry to the log detailing how long it took.
-     *
-     * @param string   $message
-     * @param callable $operation
-     * @param array    $arguments
-     *
-     * @return void
-     */
-    public function writeTimedLog($message, $operation, array $arguments = array())
-    {
-        $this->write(sprintf('%-66.66s .. ', $message));
-        $timerStart = microtime(true);
-
-        call_user_func_array($operation, $arguments);
-
-        $this->writeln(sprintf('%8.3fs', microtime(true) - $timerStart));
-    }
-
-    /**
-     * Write an entry to the console and to the provided logger.
-     *
-     * @param array|string $messages
-     * @param bool         $newline
-     * @param int          $type
-     *
-     * @return void
-     */
-    public function write($messages, $newline = false, $type = 0)
-    {
-        $messages = (array) $messages;
-
-        if ($this->getLogger()) {
-            foreach ($messages as $message) {
-                $this->getLogger()->info($this->getFormatter()->format(strip_tags($message)));
-            }
-        }
-
-        parent::write($messages, $newline, $type);
-    }
-}
diff --git a/src/phpDocumentor/Transformer/Command/Project/TransformCommand.php b/src/phpDocumentor/Transformer/Command/Project/TransformCommand.php
index d9677769c2..d709ee9339 100644
--- a/src/phpDocumentor/Transformer/Command/Project/TransformCommand.php
+++ b/src/phpDocumentor/Transformer/Command/Project/TransformCommand.php
@@ -31,7 +31,6 @@
 use Symfony\Component\Console\Output\OutputInterface;
 use Symfony\Component\Filesystem\Filesystem;
 use Zend\Cache\Storage\StorageInterface;
-use Zend\Stdlib\AbstractOptions;
 
 /**
  * Transforms the structure file into the specified output format
@@ -185,16 +184,18 @@ protected function execute(InputInterface $input, OutputInterface $output)
 
         $projectDescriptor = $this->getBuilder()->getProjectDescriptor();
         $mapper = new ProjectDescriptorMapper($this->getCache());
-        $output->writeTimedLog('Load cache', array($mapper, 'populate'), array($projectDescriptor));
+        $this->writeTimedLog($output,'Load cache', array($mapper, 'populate'), array($projectDescriptor));
 
         foreach ($this->getTemplates($input) as $template) {
-            $output->writeTimedLog(
+            $this->writeTimedLog(
+                $output,
                 'Preparing template "'. $template .'"',
                 array($transformer->getTemplates(), 'load'),
                 array($template, $transformer)
             );
         }
-        $output->writeTimedLog(
+        $this->writeTimedLog(
+            $output,
             'Preparing ' . count($transformer->getTemplates()->getTransformations()) . ' transformations',
             array($this, 'loadTransformations'),
             array($transformer)
@@ -206,7 +207,7 @@ protected function execute(InputInterface $input, OutputInterface $output)
 
         /** @var CompilerPassInterface $pass */
         foreach ($this->compiler as $pass) {
-            $output->writeTimedLog($pass->getDescription(), array($pass, 'execute'), array($projectDescriptor));
+            $this->writeTimedLog($output, $pass->getDescription(), array($pass, 'execute'), array($projectDescriptor));
         }
 
         if ($progress) {
@@ -223,7 +224,7 @@ protected function execute(InputInterface $input, OutputInterface $output)
      */
     protected function getCache()
     {
-        return $this->getContainer()->offsetGet('descriptor.cache');
+        return $this->getContainer()->get('descriptor.cache');
     }
 
     /**
diff --git a/tests/unit/phpDocumentor/ApplicationTest.php b/tests/unit/phpDocumentor/ApplicationTest.php
deleted file mode 100644
index 306919c8f5..0000000000
--- a/tests/unit/phpDocumentor/ApplicationTest.php
+++ /dev/null
@@ -1,213 +0,0 @@
-<?php
-
-namespace phpDocumentor;
-
-use Mockery as m;
-use Monolog\Logger;
-use Symfony\Component\Console\Application as ConsoleApplication;
-
-class ApplicationTest extends \Mockery\Adapter\Phpunit\MockeryTestCase
-{
-    /** @var Application */
-    private $fixture;
-
-    /**
-     * Initializes the fixture for this test.
-     */
-    public function setUp()
-    {
-        $this->fixture = new Application();
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfStopwatchIsStarted()
-    {
-        $this->assertTrue(isset($this->fixture['kernel.timer.start']));
-        $this->assertTrue(isset($this->fixture['kernel.stopwatch']));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfVersionIsPopulated()
-    {
-        $this->assertRegExp('/^[\d]+\.[\d]+\.[\d]+(\-[\w]+)?$/', Application::$VERSION);
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfSerializerIsRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['serializer']));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfConfigurationIsRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['config']));
-        $this->assertInstanceOf('phpDocumentor\Configuration', $this->fixture['config']);
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     * @covers phpDocumentor\Application::addEventDispatcher
-     */
-    public function testIfEventDispatcherIsRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['event_dispatcher']));
-        $this->assertInstanceOf('phpDocumentor\Event\Dispatcher', $this->fixture['event_dispatcher']);
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfTranslatorIsRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['translator']));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfDescriptorBuilderIsRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['descriptor.builder']));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfParserIsRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['parser']));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfPartialsAreRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['partials']));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfTransformerIsRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['transformer']));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     */
-    public function testIfPluginsAreRegistered()
-    {
-        $this->assertTrue(isset($this->fixture['transformer.writer.collection']['checkstyle']));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     * @covers phpDocumentor\Application::addCommandsForProjectNamespace
-     */
-    public function testIfRunCommandIsRegistered()
-    {
-        /** @var ConsoleApplication $console */
-        $console = $this->fixture['console'];
-        $this->assertTrue($console->has('project:run'));
-    }
-
-    /**
-     * @covers phpDocumentor\Application::__construct
-     * @covers phpDocumentor\Application::defineIniSettings
-     */
-    public function testIfMemoryLimitIsDisabled()
-    {
-        $this->assertSame('-1', ini_get('memory_limit'));
-    }
-
-    /**
-     * Test setting loglevel to logger.
-     *
-     * @param string $loglevel
-     * @param string $expectedLogLevel
-     *
-     * @dataProvider loglevelProvider
-     * @covers phpDocumentor\Application::configureLogger
-     */
-    public function testSetLogLevel($loglevel, $expectedLogLevel)
-    {
-        $logger = m::mock('Monolog\Logger')
-            ->shouldReceive('pushHandler')->with(m::on(function($stream) use($expectedLogLevel) {
-               if (!$stream instanceof \Monolog\Handler\StreamHandler) {
-                   return false;
-               }
-
-               return $stream->getLevel() == $expectedLogLevel;
-            }))
-            ->shouldReceive('popHandler')
-            ->getMock();
-        $this->fixture->configureLogger($logger, $loglevel);
-        $this->assertSame($expectedLogLevel, $this->fixture['monolog.level']);
-    }
-
-    /**
-     * Data provider for testSetLogLevel
-     *
-     * @return array[]
-     */
-    public function loglevelProvider()
-    {
-        return array(
-            array(
-                'emergency',
-                Logger::EMERGENCY,
-            ),
-            array(
-                'emerg',
-                Logger::EMERGENCY,
-            ),
-            array(
-                'alert',
-                Logger::ALERT,
-            ),
-            array(
-                'critical',
-                Logger::CRITICAL,
-            ),
-            array(
-                'error',
-                Logger::ERROR,
-            ),
-            array(
-                'err',
-                Logger::ERROR,
-            ),
-            array(
-                'warning',
-                Logger::WARNING,
-            ),
-            array(
-                'warn',
-                Logger::WARNING,
-            ),
-            array(
-                'notice',
-                Logger::NOTICE,
-            ),
-            array(
-                'info',
-                Logger::INFO,
-            ),
-            array(
-                'debug',
-                Logger::DEBUG,
-            ),
-        );
-    }
-}
diff --git a/tests/unit/phpDocumentor/BootstrapTest.php b/tests/unit/phpDocumentor/BootstrapTest.php
deleted file mode 100644
index 45459316b3..0000000000
--- a/tests/unit/phpDocumentor/BootstrapTest.php
+++ /dev/null
@@ -1,136 +0,0 @@
-<?php
-/**
- * phpDocumentor
- *
- * PHP Version 5.3
- *
- * @copyright 2010-2018 Mike van Riel / Naenius (http://www.naenius.com)
- * @license   http://www.opensource.org/licenses/mit-license.php MIT
- * @link      http://phpdoc.org
- */
-namespace phpDocumentor;
-
-use org\bovigo\vfs\vfsStream;
-use org\bovigo\vfs\vfsStreamDirectory;
-use PHPUnit\Framework\TestCase;
-
-/**
- * Test class for \phpDocumentor\Bootstrap.
- *
- * @covers phpDocumentor\Bootstrap
- */
-class BootstrapTest extends \Mockery\Adapter\Phpunit\MockeryTestCase
-{
-    /**
-     * Directory structure when phpdocumentor is installed using composer.
-     *
-     * @var array
-     */
-    protected $composerInstalledStructure = array(
-        'dummy' => array(
-            'vendor' => array(
-                'phpDocumentor' => array(
-                    'phpDocumentor' => array(
-                        'src' => array(
-                            'phpDocumentor' => array(),
-                        ),
-                    ),
-                ),
-            ),
-        ),
-    );
-
-    /**
-     * Directory structure when phpdocumentor is installed from git.
-     *
-     * @var array
-     */
-    protected $standaloneStructure = array(
-        'dummy' => array(
-            'vendor' => array(),
-            'src' => array(
-                'phpDocumentor' => array(),
-            ),
-            'test' => array(),
-        ),
-    );
-
-    /**
-     * @covers phpDocumentor\Bootstrap::createInstance
-     */
-    public function testCreatingAnInstanceUsingStaticFactoryMethod()
-    {
-        $this->assertInstanceOf('phpDocumentor\Bootstrap', Bootstrap::createInstance());
-    }
-
-    /**
-     * @covers phpDocumentor\Bootstrap::initialize
-     */
-    public function testInitializingTheApplication()
-    {
-        $bootstrap = Bootstrap::createInstance();
-        $this->assertInstanceOf('phpDocumentor\Application', $bootstrap->initialize());
-    }
-
-    /**
-     * @covers phpDocumentor\Bootstrap::findVendorPath
-     */
-    public function testFindVendorPathStandAloneInstall()
-    {
-        vfsStream::setup('root', null, $this->standaloneStructure);
-        $bootstrap = Bootstrap::createInstance();
-
-        $baseDir = vfsStream::url('root/dummy/src/phpDocumentor');
-        $this->assertSame('vfs://root/dummy/src/phpDocumentor/../../vendor', $bootstrap->findVendorPath($baseDir));
-    }
-
-    /**
-     * @covers phpDocumentor\Bootstrap::findVendorPath
-     */
-    public function testFindVendorPathComposerInstalled()
-    {
-        $root = vfsStream::setup('root', null, $this->composerInstalledStructure);
-        vfsStream::newFile('composer.json')->at($root->getChild('dummy'));
-
-        $bootstrap = Bootstrap::createInstance();
-        $baseDir = vfsStream::url('root/dummy/vendor/phpDocumentor/phpDocumentor/src/phpDocumentor');
-        $this->assertSame(
-            'vfs://root/dummy/vendor/phpDocumentor/phpDocumentor/src/phpDocumentor/../../../../../vendor'
-            , $bootstrap->findVendorPath($baseDir)
-        );
-    }
-
-    /**
-     * Tests if exception is thrown when no autoloader is present
-     *
-     * @expectedException \RuntimeException
-     * @covers phpDocumentor\Bootstrap::createAutoloader
-     */
-    public function testCreateAutoloaderNoAutoloader()
-    {
-        vfsStream::setup('root', null, $this->standaloneStructure);
-        $bootstrap = Bootstrap::createInstance();
-        $bootstrap->createAutoloader(vfsStream::url('root/dummy/vendor'));
-    }
-
-    /**
-     * checks autoload.php is required and returned by createAutoloader
-     *
-     * @covers phpDocumentor\Bootstrap::createAutoloader
-     */
-    public function testCreateAutoloader()
-    {
-        $root = vfsStream::setup('root', null, $this->standaloneStructure);
-
-        /** @var vfsStreamDirectory $firstChild */
-        $firstChild = $root->getChild('dummy');
-        $secondChild = $firstChild->getChild('vendor');
-
-        vfsStream::newFile('autoload.php')->withContent('<?php return true;')
-            ->at($secondChild);
-
-        $bootstrap = Bootstrap::createInstance();
-        $this->assertTrue($bootstrap->createAutoloader(vfsStream::url('root/dummy/vendor')));
-    }
-
-}