Publishing didn't change the url of the js file?

I have two targets defined.
Development which is http://localhost/~username/projectname

Production: https://subdomain.domain.com/

However, when I published it all of the included files such as font-awesome.min.css are returning 404 errors because they still reference /~username/projectname on the production server.

So I’ve obviously done somethin wrong. I changed Links relative to = site root, it was document root.

What i see in console:
https://sub.domain.com/~username/projectname/font-awesome.min.css

what it should have been:
https://sub.domain.com/fontawesome4/css/font-awesome.min.css