(PUP-3069) Clear configuration_file for tests

The new default_manifest integration spec is parsing actual
configuration files and uncovered that our Settings do not clear the
@configuration_file data when #unsafe_clear is called. This allows
parsed settings to leak across specs.

Specifically dropping the @configuration_file in the test helper
Settings#clear_everything_for_tests, resolves this, without changing the
behavior of the Settings#clear, and through it, the Puppet.clear
methods.