Restructuring the phases of configuration.
Tweaks to restructuring phases of application.
Refactor of config and its purpose and behavior.
Some tidying up.
Some tweaks to tests and added loading of appropriate application files automatically.
Modules try to automatically load their services.yml file if it exists.
Added missing test for Application->getApplicationDir().
Further config changes, but only how it is used in the framework. Moved some services definitions to yml file.