Refactor filesystem, Drush, shell utilities

No [deliberate, significant] functional change.

The ultimate aim is to get rid of the PlatformCommand and EnvironmentCommand classes.

Tests on my fork - https://travis-ci.org/pjcdawkins/platformsh-cli

Latest Scrutinizer inspection - https://scrutinizer-ci.com/g/pjcdawkins/platformsh-cli/?branch=refactoring

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