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You can install without hitting install_settings_form_submit() if your settings.php already has the db stuff in it, and right now in that case your config directory never gets created. This results in config files being created in sites/default/files.
Current thinking would be to make the installer bail out with an error if you have a settings.php already but it doesn't contain a $config_file_directory.
Comments
Comment #1
alexpottAdd tag
Comment #2
gddDuplicate of #1464944: Installation of configuration system fails in some cases