Previously the PDK::Config class could only read (get) values, it could not set
them easily, and lacked logic to deal with different value types, for example
if you set a deep hash value, then the save data method on the namespace was
not triggered.

This commit:

* Adds a PDK::Config.set method which takes into account nested namespaces,
  setting deep hashes, creates missing hash structures, and can add to, or
  explicitly set array, values.  All of this is necessary for the CLI component

* Adds tests for the different scenarios

Now that the PDK::Config class now has a set method, we can add a `set config`
CLI command so users can set configuration values.  Later commits will add the
`remove config` CLI command.

This commit:
* Adds the basic `pdk set config` command
* Adds type conversion using the `--type` parameter
* Adds tests for the CLI command

Previously there were no full tests for the get and set configuration.  This
commit adds package-testing tests which modifies configuration files on actual
systems during testing.

Previously many calls within the PDK used `.user` directly.  However now that
there is a formal get and set method, accessing these directly is no longer
required and is a private API.  This commit updates any references to these
private methods and changes them to use .get and .set appropriately.

This commit updates the tests to use the anything matchcer instead of Object as
per recommended practice in rspec-mocks.