diff --git a/scripts/install b/scripts/install
index af3effd..023c7dc 100755
--- a/scripts/install
+++ b/scripts/install
@@ -122,8 +122,8 @@ chown -R $app:$app "$final_path"
 ynh_script_progression --message="Building Node dependencies..." --weight=30
 
 pushd "$final_path"
-  ynh_use_nodejs
-  ynh_exec_warn_less sudo -u $app env $ynh_node_load_PATH npm install
+    ynh_use_nodejs
+    ynh_exec_warn_less sudo -u $app env $ynh_node_load_PATH npm install
 popd
 
 #=================================================
@@ -156,17 +156,6 @@ chown $app:$app "$base_config_path"
 chmod 600 "$user_config_path"
 chown $app:$app "$user_config_path"
 
-#=================================================
-# STORE THE CONFIG FILE CHECKSUM
-#=================================================
-
-# Calculate and store the config file checksum into the app settings
-ynh_store_file_checksum --file="$app_service_registration_path/$app.yaml"
-
-# Probably not worth anymore, because the overrides should
-# be now in $user_config_path
-# ynh_store_file_checksum --file="$base_config_path"
-
 #=================================================
 # SETUP SYSTEMD
 #=================================================
@@ -208,6 +197,14 @@ cp "$final_path/$app.yaml" $app_service_registration_path/$app.yaml
 /opt/yunohost/matrix-$synapse_instance/update_synapse_for_appservice.sh \
     || ynh_die "Synapse can't restart with the appservice configuration"
 
+#=================================================
+# STORE THE CONFIG FILE CHECKSUM
+#=================================================
+
+# Calculate and store the config file checksum into the app settings
+ynh_store_file_checksum --file="$app_service_registration_path/$app.yaml"
+
+
 #=================================================
 # SEND A README FOR THE ADMIN
 #=================================================
diff --git a/scripts/upgrade b/scripts/upgrade
index 3284ae6..5c8e940 100644
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -107,10 +107,10 @@ ynh_system_user_create --username=$app --home_dir="$final_path"
 
 if [ "$upgrade_type" == "UPGRADE_APP" ]
 then
-	ynh_script_progression --message="Upgrading source files..." --weight=1
+    ynh_script_progression --message="Upgrading source files..." --weight=1
 
-	# Download, check integrity, uncompress and patch the source from app.src
-	ynh_setup_source --dest_dir="$final_path"
+    # Download, check integrity, uncompress and patch the source from app.src
+    ynh_setup_source --dest_dir="$final_path" --keep="run.sh"
 fi
 
 chmod 750 "$final_path"
@@ -132,8 +132,8 @@ ynh_install_nodejs --nodejs_version=$NODEJS_VERSION
 ynh_script_progression --message="Building Node dependencies..." --weight=3
 
 pushd "$final_path"
-  ynh_use_nodejs
-  ynh_exec_warn_less sudo -u $app env $ynh_node_load_PATH npm install
+    ynh_use_nodejs
+    ynh_exec_warn_less sudo -u $app env $ynh_node_load_PATH npm install
 popd
 
 #=================================================