protected function registerModulesDir($repository, $repositoryPath)
 {
     $allDirs = \Jelix\Core\App::getDeclaredModulesDir();
     $path = realpath($repositoryPath);
     if ($path == '') {
         throw new Exception('The modules dir ' . $repository . ' is not a valid path');
     }
     $path = jFile::shortestPath(\Jelix\Core\App::appPath(), $path);
     $found = false;
     foreach ($allDirs as $dir) {
         $dir = jFile::shortestPath(\Jelix\Core\App::appPath(), $dir);
         if ($dir == $path) {
             $found = true;
             break;
         }
     }
     // the modules dir is not known, we should register it.
     if (!$found) {
         $this->createDir($repositoryPath);
         if (file_exists(\Jelix\Core\App::appPath('composer.json')) && file_exists(\Jelix\Core\App::appPath('vendor'))) {
             // we update composer.json
             $json = json_decode(file_get_contents(\Jelix\Core\App::appPath('composer.json')), true);
             if (!$json) {
                 throw new Exception('composer.json has bad json format');
             }
             if (!isset($json['extra'])) {
                 $json['extra'] = array('jelix' => array('modules-dir' => array()));
             } else {
                 if (!isset($json['extra']['jelix'])) {
                     $json['extra']['jelix'] = array('modules-dir' => array());
                 } else {
                     if (!isset($json['extra']['jelix']['modules-dir'])) {
                         $json['extra']['jelix']['modules-dir'] = array();
                     }
                 }
             }
             $json['extra']['jelix']['modules-dir'][] = $path;
             file_put_contents(\Jelix\Core\App::appPath('composer.json'), json_encode($json, JSON_PRETTY_PRINT));
             if ($this->verbose()) {
                 echo "The given modules dir has been added into your composer.json\n";
             }
             echo "You should launch 'composer update' to have your module repository recognized\n";
         } else {
             if (file_exists(\Jelix\Core\App::appPath('application.init.php'))) {
                 // we modify the application.init.php directly
                 $content = file_get_contents(\Jelix\Core\App::appPath('application.init.php'));
                 $content .= "\n\\Jelix\\Core\\App::declareModulesDir(__DIR__.'/" . $path . "');\n";
                 file_put_contents(\Jelix\Core\App::appPath('application.init.php'), $content);
                 if ($this->verbose()) {
                     echo "The given modules dir has been added into your application.init.php\n";
                 }
             }
         }
     }
 }