説明がわかりにくくて申し訳ありません。

ec-cubeのcomposer.jsonなどがあるディレクトリで
composer update symfony/flex --no-plugins --no-scripts
を行ったら、以下の文言がでてきて、相変わらず、プラグインの有効ボタンなどが表示されない状態です。次にどんなことをすればよいかご教示いただけますでしょうか。

Loading composer repositories with package information
Updating dependencies (including require-dev)
Package operations: 9 installs, 1 update, 0 removals
- Updating symfony/flex (v1.1.8 => v1.4.1): Downloading (100%)
- Installing ec-cube/eccube4lineloginintegration (1.1.0): Downloading (100%)
- Installing ec-cube/sprockettag (1.0.0): Downloading (100%)
- Installing ec-cube/cartclearv4 (1.0.1): Downloading (100%)
- Installing ec-cube/mgsocialbutton (1.0.1): Downloading (100%)
- Installing ec-cube/mailmagazine4 (4.0.1): Downloading (100%)
- Installing ec-cube/maker4 (4.0.1): Downloading (100%)
- Installing ec-cube/productreview4 (4.0.1): Downloading (100%)
- Installing ec-cube/recommendedproducts4 (1.0.3): Downloading (100%)
- Installing ec-cube/relatedproduct4 (4.0.1): Downloading (100%)
Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested.
Package symfony/lts is abandoned, you should avoid using it. Use symfony/flex instead.
Writing lock file
Generating optimized autoload files
Warning: Ambiguous class resolution, "Eccube\Entity\Product" was found in both "$baseDir . '/app/proxy/entity/Product.php" and "/home/drugpure/drugpure.jp/public_html/src/Eccube/Entity/Product.php", the first will be used.