Deprecate `Config::addScopedProperties`

Use `::set` instead.

This drove out fixing some things about `Config::set`:
* With a null key-path, it now sets the root object
* `::unset` now works with a `source` but no `scopeSelector`
* `editor.completions` now needs to be part of the built-in schema, because many packages write to that key-path as a scoped property.