why is jenkins removing empty directories from downloaded git repo?

I'm using Jenkins to deploy a Laravel application to Elastic Beanstalk AWS service.

Its working fine but for some reason the zip file that is being created by Jenkins doesn't contains directories which has only .gitignore file inside. Example:

/bootstrap
    app.php
    /cache
        .gitignore
/storage
    /app
        .gitignore
    /framework
        .gitignore
    /logs
        .gitignore

None of these directories with .gitignore are present in zip file generated by Jenkins and this is causing errors in AWS.

Maybe should I set some configuration on git clone command in Jenkins?

via Chebli Mohamed