skeleton VS adr-example

The php-pds/skeleton repository is a great document to learn how to structure your code in PHP, but it doesn't show how to organize your code inside the src/ folder.

Structuring the rest of the project, I would follow https://github.com/php-pds/skeleton

At first glance, this appears mostly compliant with the pds/skeleton publication. Maybe consider putting the configure.php script in an appropriate subdirectory (probably bin/). Nicely done!

First suggestion, would be to move all the php files from public. Ideally, this should all go in a /src folder - https://github.com/php-pds/skeleton

It looks like this: https://github.com/php-pds/skeleton/tree/1.0.0

Folder structure should try to follow: https://github.com/php-pds/skeleton

Adding to the above link a full ADR Example - https://github.com/pmjones/adr-example

Yes, as an example, the First Application's business logic (not that it's much) doesn't tie itself to the framework, as one example. Odan's Slim Skeleton, ADR Example (yes, I know you are the author), and the Aura Payload example class can be seen as other examples.

ADR (as opposed to MVC) - direct link - example

https://github.com/pmjones/adr-example - Follow up example to the above. ADR is an alternative to MVC

More on ADR (like MVC) - https://github.com/pmjones/adr-example

Another option, to me and speaking to the OP as an alternative, it is simpler to add some Data Mappers/Repositories to abstract away the Database code. Good examples is the sample ADR application, Payload library example, Slim 3 First Application, or this Slim 4 Skeleton application

Simple example of a MVC/ADR (Action-Domain-Responder, similar to MVC) system - https://github.com/pmjones/adr-example

Call your class (which doesn't look like a controller anymore...), then, output it to your HTML or JSON renderer, based on the check. You can do this in a class (or 2 - look up ADR - https://github.com/pmjones/adr-example) or in the router.