Manage site settings after creation

Let's say I have created a site with /public as the web directory.

Once it has been created, if I want to change this directory, I must edit the vhost file... Not so convenient, but let's go with this.

I edit this, now my site works.

Now let's add a letsencrypt certificate . The vhost is changed and my root folder is not the one I set anymore :(

-> we should be able to change the site settings that is used to generate the vhost file.