Parse configuration using InputInterface passed to Application

Currently the `Console\Application` retrieves a configuration file path from a newly create `ArgvInput`. If a customised `InputInterface` is passed to `Application::run`, any configuration file set is ignored. This commit uses the `InputInterface` passed to the application to load configuration.

Please advise on how best to test this! I'm new to PhpSpec and BDD. The existing specs and features run, though I can't see any specific to the `Application` class. The `loadConfigurationFile` and `parseConfigurationFile` methods are protected so I can't test them directly.

M