Consider an MVC framework? #93
Description
Frameworks like Laravel or CakePHP might be able to provide some structure and convention to the project, making it easier for folks to get oriented in the code and make contributions. This also serves to centralize things like a public/ folder to serve as a web root, a project-wide DB connection and ORM (allowing you to move away from raw SQL strings), separating business logic and display logic into easier to edit controllers and "views", grouping assets into a more standardized folder structure and build process and leveraging the output of a larger community to help provide security and best practices.
Obviously ease of maintenance and understanding the code for the owner is paramount and that supersedes anything I mentioned above, but it'd be an interesting experiment to try. The big missing piece is the DB schema, I think. I suspect a lot of the manual mixed PHP and HTML would probably become more understandable inside one of these frameworks.