Repair problems with shipped apps on update

repair-appconfig.php

<?php
/**
 * @copyright Copyright (c) 2016 Joas Schilling <coding@schilljs.com>
 *
 * @license GNU AGPL version 3 or any later version
 *
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 *
 */

die('Do not execute this, unless you have been directly adviced to do so!');

require_once __DIR__ . '/lib/base.php';

foreach (\OC::$APPSROOTS as $app_dir) {
	if ($dir = opendir($app_dir['path'])) {
		while (false !== ($filename = readdir($dir))) {
			if (substr($filename, 0, 1) != '.' && is_dir($app_dir['path'] . "/$filename")) {
				if (file_exists($app_dir['path'] . "/$filename/appinfo/info.xml")) {
					if (\OC::$server->getConfig()->getAppValue($filename, "installed_version", null) === null) {
						$info = \OC_App::getAppInfo($filename);
						$enabled = isset($info['default_enable']);
						if (($enabled || in_array($filename, \OC::$server->getAppManager()->getAlwaysEnabledApps()))
							&& \OC::$server->getConfig()->getAppValue($filename, 'enabled') !== 'no') {
							echo 'Fixing missing records for app: ' . $filename;
							installOrUpdateShippedApp($filename);
							\OC::$server->getConfig()->setAppValue($filename, 'enabled', 'yes');
							echo 'Fixed missing records for app: ' . $filename;
						}
					}
				}
			}
		}
		closedir( $dir );
	}
}

function installOrUpdateShippedApp($app) {
	//install the database
	$appPath = \OC_App::getAppPath($app);
	if (is_file("$appPath/appinfo/database.xml")) {
		try {
			\OC_DB::createDbFromStructure("$appPath/appinfo/database.xml");
		} catch (\Doctrine\DBAL\Exception\TableExistsException $e) {
			\OC_DB::updateDbFromStructure("$appPath/appinfo/database.xml");
		}
	}

	//run appinfo/install.php
	\OC_App::registerAutoloading($app, $appPath);
	include "$appPath/appinfo/install.php";

	$info = OC_App::getAppInfo($app);
	if (is_null($info)) {
		return false;
	}
	\OC_App::setupBackgroundJobs($info['background-jobs']);

	\OC_App::executeRepairSteps($app, $info['repair-steps']['install']);

	$config = \OC::$server->getConfig();

	$config->setAppValue($app, 'installed_version', \OC_App::getAppVersion($app));
	if (array_key_exists('ocsid', $info)) {
		$config->setAppValue($app, 'ocsid', $info['ocsid']);
	}

	//set remote/public handlers
	foreach ($info['remote'] as $name => $path) {
		$config->setAppValue('core', 'remote_' . $name, $app . '/' . $path);
	}
	foreach ($info['public'] as $name => $path) {
		$config->setAppValue('core', 'public_' . $name, $app . '/' . $path);
	}

	\OC_App::setAppTypes($info['id']);

	if (isset($info['settings']) && is_array($info['settings'])) {
		// requires that autoloading was registered for the app,
		// as happens before running the install.php some lines above
		\OC::$server->getSettingsManager()->setupSettings($info['settings']);
	}

	return $info['id'];
}