JHipster introduced a nice upgrade utility since version 3.4 but it seems it has some issue when you work in Ubuntu.
This is a workaround to get it working
Install JHipster in Ubuntu 16
JHipster
JHipster is a Yeoman generator that will kick start your AngularJS -Java Spring project. It can create all your user administration services (including facebook, twitter and google user types). It can create a bunch of files to handle your entities with a single command (Spring controllers, repositories, REST controller, Angular controllers, forms, views, dialogs and tests)
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