Generate config file before setting up data dir. Make mysql_install_data use config

This is required if a few of the `innodb` values are modified (as per https://dev.mysql.com/doc/refman/5.6/en/mysql-install-db.html). `innodb_data_file_path` being one of the bigger ones.

Had to remove the ChefSpec `run_execute` call for datadir setup since it isn't registered anymore in the same way. I check for the notify at least. Let me know if there is a way I can ensure it actually does (or doesn't to test the `not_if`) get ran.