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Committing this because I'm at a stage where I can connect to MySQL from PHP and perform basic queries. I had to change MySQL's authentication method on my local machine described [here](https://serverfault.com/questions/924367/php-7-2-8-pdo-fails-to-connect-to-mysql-8-0-12-ga-in-aws-ec2-lemp-stack/939903#939903), the other changes were just fixing minor bugs in directory paths.