Stop accepting loose files

What does this Merge Request do and why?

Configuring GDK through gdk.yml was introduced in the summer of 20191. It's time we make this the only way to configure GDK and get rid of the use of loose files.

With these changes the GDK config will raise an error if one of the old loose files is detected. An error might look something like this:

❌️ ERROR: Your gdk.yml is invalid.

Loose file [webpack_port] is no longer allowed.
Instead set webpack.port in your gdk.yml

It's a shortcut to #1273, which I think is too much work and has too many risks. It has been long enough to go this route IMHO.

Merge Request checklist

• This change is backward compatible. If not, please include steps to communicate to our users.
• Tests added for new functionality. If not, please raise Issue to follow-up.
• Documentation added/updated, if needed.
• gdk doctor test added, if needed.
• Add the ~highlight label if this MR should be included in the CHANGELOG.md.