Isn't a root system just a folder of files?

Yes. That's the good part.

It's 3,787 files: 82 skills, 230 changes to the database, 47 functions running on their own, and 158 daily logs with none deleted.

Every one of those is a plain file. You open it, read it in English, change a line, and the system behaves differently tomorrow. Every file opens in a text editor, and it's yours whether or not you're logged in to anything.

That's also why it travels. It copies to a new laptop, and it hands over cleanly to whoever runs your operations next.