Respect `--basepath` configuration option in output

[fredden]

https://github.com/magento/magento-coding-standard/commit/9c2ac84d1fddfbc1f5c16762d42280d1b7ffaeb9 is the main purpose of this pull request. In order to get there cleanly, a number of refactoring commits were required. I recommend that this pull request is reviewed commit-by-commit, as the final change-set may be confusing.