diff --git a/README.md b/README.md
index 6eaeecc..51d6db3 100644
--- a/README.md
+++ b/README.md
@@ -25,9 +25,9 @@ or from the Web administration:
 
 ## TODO
 
- * Update the `upgrade` script and test the upgrade from the current
-   official package
+ * Test the upgrade from the current official package
  * Add `backup` and `remove` scripts
+ * Update `config.php` and `config.system.php` at upgrade
 
 ## Links ##
 
diff --git a/scripts/upgrade b/scripts/upgrade
index 61443f9..7322907 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -1,90 +1,67 @@
 #!/bin/bash
 
-# Retrieve arguments
-domain=$(sudo yunohost app setting baikal domain)
-path=$(sudo yunohost app setting baikal path)
-password=$(sudo yunohost app setting baikal password)
+set -u
 
-# Remove trailing "/" for next commands
+# Load common variables and helpers
+. ./_common.sh
+
+# Set app specific variables
+app=${!#}
+dbname=$app
+dbuser=$app
+
+# Retrieve arguments
+domain=$(ynh_app_setting_get "$app" domain)
+path=$(ynh_app_setting_get "$app" path)
 path=${path%/}
 
+# Check destination directory
+DESTDIR="/var/www/$app"
+[[ ! -d $DESTDIR ]] && ynh_die \
+"The destination directory '$DESTDIR' does not exist.\
+ The app is not correctly installed, you should remove it first."
 
-# Copy files to the right place
-final_path=/var/www/baikal
+# Create tmp directory and fetch new app inside
+TMPDIR=$(ynh_mkdir_tmp)
+extract_baikal "$TMPDIR"
 
-# let's not use a bash variable for this one...
-sudo rm -rf /var/www/baikal
+# Get Specific folder from current installation
+# FIXME: config.php and config.system.php are not updated with possible
+# new or changed configurations
+rm -rf "${TMPDIR}/Specific"
+sudo cp -r "${DESTDIR}/Specific" "$TMPDIR"
+sudo chown -hR "${USER}" "${TMPDIR}/Specific"
 
-sudo mkdir -p $final_path
-sudo cp -a ../sources/* $final_path
-sudo chown -R www-data: $final_path
-sudo su -c "curl -sS https://getcomposer.org/installer | php -- --install-dir=$final_path" -s /bin/sh www-data
-sudo su -c "cd $final_path && php composer.phar install" -s /bin/sh www-data
-sudo rm $final_path/composer*
+# Run Baikal upgrade from tmp directory
+cp -r ../sources/bin "$TMPDIR"
+php "${TMPDIR}/bin/upgrade.sh" \
+  || echo "The Baïkal upgrade failed, you should try to go to " \
+        "https://${domain}${path}/admin/install"
 
-db_pwd=$(sudo yunohost app setting baikal mysqlpwd)
-db_user=baikal
-sed -i "s@YNH_TIMEZONE@$(cat /etc/timezone)@g" ../conf/config.php
-sed -i "s@YNH_ADMIN_PASSWORDHASH@$(echo -n admin:BaikalDAV:$password | md5sum | cut -d ' ' -f 1)@g" ../conf/config.php
+# Install new app and set permissions
+sudo rm -rf "$DESTDIR"
+sudo mv "$TMPDIR" "$DESTDIR"
+sudo chown -R www-data: "$DESTDIR"
 
-sed -i "s@YNH_LOCATION@$path@g" ../conf/config.system.php
-sed -i "s@YNH_DBNAME@$db_user@g" ../conf/config.system.php
-sed -i "s@YNH_DBUSER@$db_user@g" ../conf/config.system.php
-sed -i "s@YNH_DBPWD@$db_pwd@g" ../conf/config.system.php
-encrypt_key=$(sudo yunohost app setting baikal encrypt_key)
-sed -i "s@YNH_ENCRYPTKEY@$encrypt_key@g" ../conf/config.system.php
+# Copy and set nginx configuration
+nginx_conf="/etc/nginx/conf.d/${domain}.d/${app}.conf"
+sed -i "s@#PATH#@${path}@g"        ../conf/nginx.conf
+sed -i "s@#LOCATION#@${path:-/}@g" ../conf/nginx.conf
+sed -i "s@#DESTDIR#@${DESTDIR}@g"  ../conf/nginx.conf
+sudo cp ../conf/nginx.conf "$nginx_conf"
 
-sudo cp ../conf/config.php $final_path/Specific
-sudo cp ../conf/config.system.php $final_path/Specific
+# Copy and set php-fpm configuration
+#phpfpm_conf="/etc/php5/fpm/pool.d/${app}.conf"
+#sed -i "s@#POOLNAME#@${app}@g"     ../conf/php-fpm.conf
+#sed -i "s@#DESTDIR#@${DESTDIR}/@g" ../conf/php-fpm.conf
+#sudo cp ../conf/php-fpm.conf "$phpfpm_conf"
+#sudo chown root: $phpfpm_conf
+#sudo chmod 644 $phpfpm_conf
 
-sudo chown -R root: $final_path
-sudo chown -R www-data: $final_path/Specific
-sudo find $final_path -type f | xargs sudo chmod 644
-sudo find $final_path -type d | xargs sudo chmod 755
+# Set SSOwat rules
+ynh_app_setting_set "$app" skipped_uris "/"
+ynh_app_setting_set "$app" protected_uris "/admin/"
 
-# Change variables in Baikal configuration
-sed -i "s@PATHTOCHANGE@$path@g" ../conf/nginx.conf
-sed -i "s@ALIASTOCHANGE@$final_path/html@g" ../conf/nginx.conf
-sudo cp ../conf/nginx.conf /etc/nginx/conf.d/$domain.d/baikal.conf
-sudo chown root: /etc/nginx/conf.d/$domain.d/baikal.conf
-sudo chmod 600 /etc/nginx/conf.d/$domain.d/baikal.conf
-
-# Reload Nginx and regenerate SSOwat conf
-sudo service nginx reload
-sudo yunohost app setting baikal skipped_uris -v "/"
-sudo yunohost app ssowatconf
-
-
-# 
-# # Backuping db
-# backup_path=/var/cache/yunohost/backups/baikal
-# final_path=/var/www/baikal/
-# 
-# mkdir -p $backup_path
-# sudo cp -a $final_path/Specific/* $backup_path 
-# 
-# # Copy files to the right place
-# sudo mkdir -p $final_path
-# sudo cp -a ../sources/* $final_path
-# sudo cp ../conf/nginx.conf /etc/nginx/conf.d/$domain.d/baikal.conf
-# sudo chown -R www-data:www-data $final_path
-# sudo find $final_path -type d -exec chmod 755 {} \;
-# sudo touch $final_path/Specific/ENABLE_INSTALL
-# #sudo chmod 755 $final_path/Specific
-# #sudo chmod 755 $final_path/Specific/db
-# #sudo chmod 755 $final_path/Specific/db/db.sqlite
-# 
-# # Change variables in Baikal configuration
-# sudo sed -i "s@PATHTOCHANGE@$path@g" /etc/nginx/conf.d/$domain.d/baikal.conf
-# sudo sed -i "s@ALIASTOCHANGE@$final_path/@g" /etc/nginx/conf.d/$domain.d/baikal.conf
-# 
-# sudo sed -i "s@PROJECT_BASEURI_@\"$path/\"@g" $final_path/Core/Frameworks/Baikal/Model/Config/System.php
-# 
-# # Restoring backup
-# sudo cp -a $backup_path/* $final_path/Specific
-# 
-# # Reload Nginx and regenerate SSOwat conf
-# sudo service php5-fpm restart
-# sudo service nginx reload
-# sudo yunohost app setting baikal skipped_uris -v "/"
-# sudo yunohost app ssowatconf
+# Reload services
+#sudo service php5-fpm restart || true
+sudo service nginx reload || true
diff --git a/sources/bin/upgrade.sh b/sources/bin/upgrade.sh
new file mode 100755
index 0000000..6468200
--- /dev/null
+++ b/sources/bin/upgrade.sh
@@ -0,0 +1,100 @@
+#!/usr/bin/env php
+<?php
+/***************************************************************
+*  Copyright notice
+*
+*  (c) 2013 Jérôme Schneider <mail@jeromeschneider.fr>
+*  All rights reserved
+*
+*  http://baikal-server.com
+*
+*  This script is part of the Baïkal Server project. The Baïkal
+*  Server project is free software; you can redistribute it
+*  and/or modify it under the terms of the GNU General Public
+*  License as published by the Free Software Foundation; either
+*  version 2 of the License, or (at your option) any later version.
+*
+*  The GNU General Public License can be found at
+*  http://www.gnu.org/copyleft/gpl.html.
+*
+*  This script 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 General Public License for more details.
+*
+*  This copyright notice MUST APPEAR in all copies of the script!
+***************************************************************/
+
+ini_set("session.cookie_httponly", 1);
+ini_set("log_errors", 1);
+error_reporting(E_WARNING | E_ERROR);
+
+define("BAIKAL_CONTEXT", true);
+define("BAIKAL_CONTEXT_INSTALL", true);
+define("PROJECT_CONTEXT_BASEURI", "/admin/install/");
+
+define('PROJECT_PATH_ROOT', realpath(__DIR__ . '/..') . '/' );
+
+if (!file_exists(PROJECT_PATH_ROOT . 'vendor/')) {
+    echo "Baïkal is not completely installed!\n";
+    exit(1);
+}
+
+require PROJECT_PATH_ROOT . "vendor/autoload.php";
+
+# Extend VersionUpgrade for cli usage
+class CLIUpgrade extends \BaikalAdmin\Controller\Install\VersionUpgrade {
+
+    function run() {
+        $sBaikalVersion = BAIKAL_VERSION;
+        $sBaikalConfiguredVersion = BAIKAL_CONFIGURED_VERSION;
+
+        if (BAIKAL_CONFIGURED_VERSION === BAIKAL_VERSION) {
+            $this->output("Baïkal is already configured for version " . $sBaikalVersion);
+            return true;
+        } else {
+            $this->output("Upgrading Baïkal from version " . $sBaikalConfiguredVersion . " to version " . $sBaikalVersion);
+        }
+
+        try {
+            $bSuccess = $this->upgrade(BAIKAL_CONFIGURED_VERSION, BAIKAL_VERSION);
+        } catch (\Exception $e) {
+            $bSuccess = false;
+            $this->output("Uncaught exception during upgrade: " . (string)$e);
+        }
+        if (!empty($oUpgrade->aErrors)) {
+            $this->output("Some errors occured:\n" . implode("\n - ", $oUpgrade->aErrors));
+        }
+        if (!empty($oUpgrade->aSuccess)) {
+            $this->output(implode("\n", $oUpgrade->aSuccess));
+        }
+        if ($bSuccess === false) {
+            $this->output("Error: unable to upgrade Baïkal.");
+        } else {
+            $this->output("Baïkal has been upgraded!");
+        }
+
+        return $bSuccess;
+    }
+
+    function output($message) {
+        echo $message . "\n";
+    }
+}
+
+# Bootstraping Flake
+\Flake\Framework::bootstrap();
+
+# Bootstrap BaikalAdmin
+\BaikalAdmin\Framework::bootstrap();
+
+if (!defined("BAIKAL_CONFIGURED_VERSION") || !defined("BAIKAL_ADMIN_PASSWORDHASH")) {
+    echo "Baïkal is not properly configured!\n";
+    exit(1);
+}
+
+# Run the upgrade
+$oUpgrade = new CLIUpgrade();
+if (!$oUpgrade->run()) {
+    exit(1);
+}