diff --git a/scripts/upgrade b/scripts/upgrade
index 1397325..8c9ad73 100755
--- a/scripts/upgrade
+++ b/scripts/upgrade
@@ -25,7 +25,6 @@ db_pwd=$(ynh_app_setting_get --app=$app --key=mysqlpwd)
 random_key=$(ynh_app_setting_get --app=$app --key=random_key)
 email=$(ynh_user_get_info --username=$admin --key=mail)
 phpversion=$YNH_PHP_VERSION
-timezone="$(cat /etc/timezone)"
 
 #=================================================
 # CHECK VERSION
@@ -79,16 +78,50 @@ ynh_script_progression --message="Making sure dedicated system user exists..."
 # Create a dedicated user (if not existing)
 ynh_system_user_create --username=$app --home_dir="$final_path"
 
+#=================================================
+# STANDARD UPGRADE STEPS
 #=================================================
 # DOWNLOAD, CHECK AND UNPACK SOURCE
 #=================================================
 
 if [ "$upgrade_type" == "UPGRADE_APP" ]
 then
-	ynh_script_progression --message="Upgrading source files..."
+  if [ `cd $final_path && git rev-parse --is-inside-work-tree` ];
+  then
+	pushd "$final_path"
+	ynh_setup_source --dest_dir=$final_path
+	ynh_secure_remove --file="$final_path/bootstrap/cache/*"
+	ynh_secure_remove --file="$final_path/vendor/"
+	popd
 
-	# Download, check integrity, uncompress and patch the source from app.src
-	ynh_setup_source --dest_dir="$final_path" --keep="$final_path/.env $final_path/storage/upload $final_path/storage/export" 
+  else
+    ynh_script_progression --message="Upgrading source files..."
+    # Create a temporary directory
+    tmpdir="$(mktemp -d)"
+
+    # Backup the config file in the temp dir
+	mkdir -p "$tmpdir/storage/upload"
+	mkdir -p "$tmpdir/storage/export"
+	mkdir -p "$final_path/storage/upload/"
+	mkdir -p "$final_path/storage/export/"
+	cp -aT "$final_path/storage/upload" "$tmpdir/storage/upload/$"
+	cp -a "$final_path/.env" "$tmpdir/.env"
+	cp -aT "$final_path/storage/export" "$tmpdir/storage/export/"
+	ynh_secure_remove --file="$final_path"
+
+	# Download, check integrity, uncompress and patch the source from app.src   
+    	ynh_setup_source --dest_dir=$final_path
+    	ynh_secure_remove  bootstrap/cache/*
+	
+	# Restore the config file and data
+	mkdir -p "$final_path/storage/upload/"
+	mkdir -p "$final_path/storage/export/"
+	cp -aT "$tmpdir/storage/upload" "$final_path/storage/upload"
+	cp -aT "$tmpdir/storage/export"  "$final_path/storage/export"
+	cp -a "$tmpdir/.env" "$final_path/.env"
+	# Remove temporary directory
+	ynh_secure_remove --file="$tmpdir"
+  fi
 fi
 
 chmod 750 "$final_path"