The document-centric model of desktop applications largely originates from the early Mac. How do you open a document in a desktop OS? You double-click on the document, and the OS finds the correct application to open it with. That was a Mac thing. On most other systems of the mid-1980s, you run your application program (from the command line) and then tell the program to load a file.
Applications as “bundles” of code and data was a Mac thing too, starting with the resource/code division in the classic Mac System. Rather than an application coming with a mess of directories of libraries and data files, it’s all bundled up into a single application file that can contain structured data (“resources”) for the GUI elements. On a classic Mac, you could load an application program up in ResEdit and modify the menus, add keyboard shortcuts, and so on, without recompiling anything.
The Apple Newton had data persistence of a sort that we now expect on cloud applications like Google Docs. Rather than “saving” and “loading” files, every change was automatically committed to storage. If you turn the device off (or it runs out of battery power), you don’t lose your work.