Is there a tutorial about programming in .pl files instead of Prolog shell?
Don’t really know of a dedicated one to just that topic.
Those are really very basic introductions. I learned by translating my skills from using other programming language IDEs to using SWI-Prolog with Visual Studio Code for editing, and the SWI-Prolog top level (swipl) for executing and debugging. Note that SWI-Prolog does come with Program Development Tools.
We could use a Wiki page for that. You are welcome to create it. I would need (as admin) to create the empty topic to get you started.