diff --git a/conf/config.dist.php b/conf/config.dist.php
index cdb7787..2101880 100644
--- a/conf/config.dist.php
+++ b/conf/config.dist.php
@@ -46,7 +46,7 @@ $providers = array(
 // CUSTOM_PROVIDER$providers += array(
 // CUSTOM_PROVIDER  '__PROVIDER__'  => array(
 // CUSTOM_PROVIDER    'name'                       => "__PROVIDER__",
-// CUSTOM_PROVIDER    'url'                        => "__INSTANCE__",
+// CUSTOM_PROVIDER    'url'                        => "__ETHERPAD_INSTANCE__",
 // CUSTOM_PROVIDER    'default_text'               => "Get involved with Etherpad at http://etherpad.org",
 // CUSTOM_PROVIDER    'markdown'                   => true,
 // CUSTOM_PROVIDER    'html'                       => true,
@@ -54,9 +54,9 @@ $providers = array(
 // CUSTOM_PROVIDER);
 
 $options = array(
-  'name'                            => "Libreto",  
+  'name'                            => "Libreto",
   'root'                            => '__PATH__',
   'use_subdomain'                   => false,
-  'default_provider'                => "__PROVIDER__",
+  'default_provider'                => "__DEFAULT_PROVIDER__",
   'providers'                       => $providers,
 );
diff --git a/conf/nginx.conf b/conf/nginx.conf
index dadb362..4d7e371 100644
--- a/conf/nginx.conf
+++ b/conf/nginx.conf
@@ -2,21 +2,21 @@
 location __PATH__/ {
 
   # Path to source
-  alias __INSTALL_DIR__/;
+  alias __INSTALL_DIR__/libreto/;
 
   index index.php;
-  
+
   # Common parameter to increase upload size limit in conjunction with dedicated php-fpm file
   client_max_body_size 50M;
 
   location __PATH__/assets/ {
-     alias __INSTALL_DIR__/libreto/assets/;
+     alias __INSTALL_DIR__/libreto/libreto/assets/;
   }
 
   # IF YOU CHANGE SOMETHING IN THIS CONFIGURATION
   # PLEASE CHECK THAT LIBRETO IS WORKING AND NOT JUST THE FIRST PAGE
   try_files "" @libreto;
-  
+
   # Include SSOWAT user panel.
   include conf.d/yunohost_panel.conf.inc;
 }
@@ -27,5 +27,5 @@ location @libreto {
     fastcgi_index index.php;
     include fastcgi_params;
     fastcgi_param REMOTE_USER $remote_user;
-    fastcgi_param SCRIPT_FILENAME __INSTALL_DIR__/index.php;
+    fastcgi_param SCRIPT_FILENAME __INSTALL_DIR__/libreto/index.php;
 }
diff --git a/manifest.toml b/manifest.toml
index 351dcdb..95f71e1 100644
--- a/manifest.toml
+++ b/manifest.toml
@@ -1,3 +1,5 @@
+#:schema https://raw.githubusercontent.com/YunoHost/apps/master/schemas/manifest.v2.schema.json
+
 packaging_format = 2
 
 id = "libreto"
@@ -52,6 +54,13 @@ ram.runtime = "50M"
     default = true
 
 [resources]
+    [resources.sources.main]
+    # This is not used as we are using git clone + submodules. It's only here for autoupdate.
+    url = "https://codeload.github.com/zamentur/libreto/zip/76408f5e98a68156afa47996e670d110a1c6106d"
+    sha256 = "4381428a38a0262b98b44b0de0d7cea35dae67049f0efe6dffff655f17d4fbda"
+    prefetch = false
+    autoupdate.strategy = "latest_github_commit"
+
     [resources.system_user]
 
     [resources.install_dir]
diff --git a/scripts/install b/scripts/install
index 810608c..9975e71 100755
--- a/scripts/install
+++ b/scripts/install
@@ -17,49 +17,18 @@ source /usr/share/yunohost/helpers
 path="/"
 ynh_app_setting_set --app="$app" --key=path --value="$path"
 
-#=================================================
-# STORE SETTINGS FROM MANIFEST
-#=================================================
-
-ynh_app_setting_set --app=$app --key=etherpad_instance --value=$etherpad_instance
-ynh_app_setting_set --app=$app --key=creation_open --value=$creation_open
-
 #=================================================
 # DOWNLOAD, CHECK AND UNPACK SOURCE
 #=================================================
 ynh_script_progression --message="Setting up source files..." --weight=4
 
-git config --system --add safe.directory $install_dir
-
 # Note: We use git instead of ynh_setup_source, cause this repo use submodules
-git clone https://github.com/zamentur/libreto.git "$install_dir" --quiet
-
-chown -R $app:www-data "$install_dir"
-
-pushd "$install_dir"
-    ynh_exec_as $app git checkout $COMMIT --quiet
-    ynh_exec_as $app git submodule update --init --recursive --quiet
-popd
+ynh_exec_as "$app" git clone https://github.com/zamentur/libreto.git "$install_dir/libreto" --quiet
+ynh_exec_as "$app" git -C "$install_dir/libreto" checkout "$COMMIT" --quiet
+ynh_exec_as "$app" git -C "$install_dir/libreto" submodule update --init --recursive --quiet
 
 chmod -R o-rwx "$install_dir"
-chown -R $app:www-data "$install_dir"
-
-#=================================================
-# PHP-FPM CONFIGURATION
-#=================================================
-ynh_script_progression --message="Configuring PHP-FPM..." --weight=2
-
-# Create a dedicated PHP-FPM config
-ynh_add_fpm_config --usage=low --footprint=low
-
-#=================================================
-# NGINX CONFIGURATION
-#=================================================
-ynh_script_progression --message="Configuring NGINX web server..." --weight=2
-
-# Create a dedicated NGINX config
-ynh_add_nginx_config
-ynh_replace_string --match_string="__INSTANCE__" --replace_string="$etherpad_instance" --target_file="/etc/nginx/conf.d/$domain.d/$app.conf"
+chown -R "$app:www-data" "$install_dir"
 
 #=================================================
 # SPECIFIC SETUP
@@ -68,19 +37,27 @@ ynh_replace_string --match_string="__INSTANCE__" --replace_string="$etherpad_ins
 #=================================================
 ynh_script_progression --message="Adding a configuration file..."
 
-cp "../conf/config.dist.php" "$install_dir/config.php"
-
-provider="${domain%%.*}"
+default_provider="framapad"
+commented_provider="// CUSTOM_PROVIDER"
 if [ "$etherpad_instance" != "https://annuel2.framapad.org" ]; then
-    ynh_replace_string --match_string="// CUSTOM_PROVIDER" --replace_string="" --target_file="$install_dir/config.php"
-    ynh_replace_string --match_string="__PROVIDER__" --replace_string="$provider" --target_file="$install_dir/config.php"
-    ynh_replace_string --match_string="__INSTANCE__" --replace_string="$etherpad_instance" --target_file="$install_dir/config.php"
-else
-    ynh_replace_string --match_string="__PROVIDER__" --replace_string="framapad" --target_file="$install_dir/config.php"
+    provider="${domain%%.*}"
+    default_provider="$provider"
+    commented_provider=""
 fi
+ynh_add_config --template="config.dist.php" --destination="$install_dir/libreto/config.php"
 
-# Calculate and store the config file checksum into the app settings
-ynh_store_file_checksum "$install_dir/config.php"
+chown "$app:www-data" "$install_dir/libreto/config.php"
+
+#=================================================
+# SYSTEM CONFIGURATION
+#=================================================
+ynh_script_progression --message="Adding system configurations related to $app..." --weight=1
+
+# Create a dedicated PHP-FPM config
+ynh_add_fpm_config --usage=low --footprint=low
+
+# Create a dedicated NGINX config
+ynh_add_nginx_config
 
 #=================================================
 # END OF SCRIPT
diff --git a/scripts/remove b/scripts/remove
index 787cb2c..5b17c2d 100755
--- a/scripts/remove
+++ b/scripts/remove
@@ -10,18 +10,13 @@ source _common.sh
 source /usr/share/yunohost/helpers
 
 #=================================================
-# REMOVE NGINX CONFIGURATION
+# REMOVE SYSTEM CONFIGURATIONS
 #=================================================
-ynh_script_progression --message="Removing NGINX web server configuration..." --weight=2
+ynh_script_progression --message="Removing system configurations related to $app..." --weight=1
 
 # Remove the dedicated NGINX config
 ynh_remove_nginx_config
 
-#=================================================
-# REMOVE PHP-FPM CONFIGURATION
-#=================================================
-ynh_script_progression --message="Removing PHP-FPM configuration..." --weight=1
-
 # Remove the dedicated PHP-FPM config
 ynh_remove_fpm_config
 
diff --git a/scripts/restore b/scripts/restore
index b080003..6fbe3e1 100755
--- a/scripts/restore
+++ b/scripts/restore
@@ -18,20 +18,15 @@ ynh_script_progression --message="Restoring the app main directory..." --weight=
 ynh_restore_file --origin_path="$install_dir"
 
 chmod -R o-rwx "$install_dir"
-chown -R $app:www-data "$install_dir"
+chown -R "$app:www-data" "$install_dir"
 
 #=================================================
-# RESTORE THE PHP-FPM CONFIGURATION
+# RESTORE SYSTEM CONFIGURATIONS
 #=================================================
-ynh_script_progression --message="Restoring the PHP-FPM configuration..." --weight=1
+ynh_script_progression --message="Restoring system configurations related to $app..." --weight=1
 
 ynh_restore_file --origin_path="/etc/php/$phpversion/fpm/pool.d/$app.conf"
 
-#=================================================
-# RESTORE THE NGINX CONFIGURATION
-#=================================================
-ynh_script_progression --message="Restoring the NGINX web server configuration..." --weight=1
-
 ynh_restore_file --origin_path="/etc/nginx/conf.d/$domain.d/$app.conf"
 
 #=================================================
@@ -41,7 +36,7 @@ ynh_restore_file --origin_path="/etc/nginx/conf.d/$domain.d/$app.conf"
 #=================================================
 ynh_script_progression --message="Reloading NGINX web server and PHP-FPM..." --weight=1
 
-ynh_systemd_action --service_name=php$phpversion-fpm --action=reload
+ynh_systemd_action --service_name="php$phpversion-fpm" --action=reload
 ynh_systemd_action --service_name=nginx --action=reload
 
 #=================================================
diff --git a/scripts/upgrade b/scripts/upgrade
index b07ed95..db5f6e0 100755
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -9,51 +9,23 @@
 source _common.sh
 source /usr/share/yunohost/helpers
 
-#=================================================
-# CHECK VERSION
-#=================================================
-
-upgrade_type=$(ynh_check_app_version_changed)
-
 #=================================================
 # STANDARD UPGRADE STEPS
 #=================================================
 # DOWNLOAD, CHECK AND UNPACK SOURCE
 #=================================================
+ynh_script_progression --message="Upgrading source files..." --weight=5
 
-if [ "$upgrade_type" == "UPGRADE_APP" ]
-then
-	ynh_script_progression --message="Upgrading source files..." --weight=5
-
-	chown -R $app:www-data "$install_dir"
-
-	# Download, check integrity, uncompress and patch the source from app.src
-	pushd "$install_dir"
-		ynh_exec_as $app git checkout master
-		ynh_exec_as $app git pull --quiet
-		ynh_exec_as $app git checkout $COMMIT --quiet
-		ynh_exec_as $app git submodule update --init --recursive --quiet
-	popd
-fi
-
-chmod -R o-rwx "$install_dir"
 chown -R $app:www-data "$install_dir"
 
-#=================================================
-# PHP-FPM CONFIGURATION
-#=================================================
-ynh_script_progression --message="Upgrading PHP-FPM configuration..." --weight=2
+# Download, check integrity, uncompress and patch the source from app.src
+ynh_exec_as "$app" git -C "$install_dir/libreto" checkout master
+ynh_exec_as "$app" git -C "$install_dir/libreto" pull --quiet
+ynh_exec_as "$app" git -C "$install_dir/libreto" checkout $COMMIT --quiet
+ynh_exec_as "$app" git -C "$install_dir/libreto" submodule update --init --recursive --quiet
 
-# Create a dedicated PHP-FPM config
-ynh_add_fpm_config --usage=low --footprint=low
-
-#=================================================
-# NGINX CONFIGURATION
-#=================================================
-ynh_script_progression --message="Upgrading NGINX web server configuration..." --weight=2
-
-# Create a dedicated NGINX config
-ynh_add_nginx_config
+chmod -R o-rwx "$install_dir"
+chown -R "$app:www-data" "$install_dir"
 
 #=================================================
 # SPECIFIC UPGRADE
@@ -63,8 +35,28 @@ ynh_add_nginx_config
 ynh_script_progression --message="Updating a configuration file..."
 
 ynh_backup_if_checksum_is_different --file="$install_dir/config.php"
-# Recalculate and store the checksum of the file for the next upgrade.
-ynh_store_file_checksum --file="$install_dir/config.php"
+
+default_provider="framapad"
+commented_provider="// CUSTOM_PROVIDER"
+if [ "$etherpad_instance" != "https://annuel2.framapad.org" ]; then
+    provider="${domain%%.*}"
+    default_provider="$provider"
+    commented_provider=""
+fi
+ynh_add_config --template="config.dist.php" --destination="$install_dir/libreto/config.php"
+
+chown "$app:www-data" "$install_dir/libreto/config.php"
+
+#=================================================
+# REAPPLY SYSTEM CONFIGURATIONS
+#=================================================
+ynh_script_progression --message="Upgrading system configurations related to $app..." --weight=1
+
+# Create a dedicated PHP-FPM config
+ynh_add_fpm_config --usage=low --footprint=low
+
+# Create a dedicated NGINX config
+ynh_add_nginx_config
 
 #=================================================
 # END OF SCRIPT
diff --git a/tests.toml b/tests.toml
index 97671ac..c35342e 100644
--- a/tests.toml
+++ b/tests.toml
@@ -1,3 +1,5 @@
+#:schema https://raw.githubusercontent.com/YunoHost/apps/master/schemas/tests.v1.schema.json
+
 test_format = 1.0
 
 [default]