fix: all private methods now protected

[benjamingrolleau]

Related issue : #327

I've just replaced all private methods by protected methods. We can now extend Scaffold_Command easily.

[danielbachhuber]

Thanks for the PR, @benjamingrolleau !

If we make these methods protected, then we're making a contract with the package consumer and have to worry about backwards-compat breaks, etc. (unlikely as it is).

Generally, when we do offer utilities, we explicitly indicate them as such, e.g. https://make.wordpress.org/cli/handbook/references/internal-api/

You're welcome to copy whatever code you'd like into your project!