Removing errant print statement from #840540.
Issue #1954898 by alexpott: Fixed site-install fails to install over an existing site because the format of config_directories[] in settings.php has changed.
Issue #1787452 by danylevskyi: drush_delete_dir() doesn't delete symlinked files by default.
Follow-up to issue #840540 to fix failing test, and copy any local patches into the patched project.