Considering how often we run into confusion while talking about Scrivener, I’ll try to make clear what I mean by certain words. I haven't always made it clear up to now, and most people never do.
Project (generic): Anything you’re trying to accomplish. Writing a book or a blog, or building a house. In a Scrivener post, I’ll call this a book, a blog, or a house — never a project.
Scrivener project: a .scriv “file” — which isn’t a file at all. It’s a folder on Windows, a package on the Mac, and gods-know-what, on iOS. It contains everything to do with what Scrivener opens so that you can edit and Compile content. If I say project on a Scrivener page, THIS is what I mean.
Mac or Windows folders, files, and packages: the contents of your hard drive, to include Scrivener packages or folders, folders and files inside a package or Scrivener folder, and other files and folders. They live independent of Scrivener (even the ones you can open in Scrivener). Every file location is a folder.
If I say system file or system folder, this is what I mean.
Document, draft, or manuscript (generic): A PDF or Word file, printed book, etc. I’ll never use “document” this way on a Scrivener post. I’ll get to Scrivener’s Manuscript/Draft a bit later.
Scrivener files, folders, documents: Files and folders are Binder documents, both can include text, and both can have documents nested in them. They’re indistinguishable except that folders have a different default icon and (depending on the template used to create a project), different default separators and settings for inclusion of text (and other settings). All these settings can be changed.
I’ll call these documents, folders, files, or text files. For most purposes, “document” is all we need to say. If I mean a hard disk file or folder, I’ll try to always say “system file” or “system folder”.
Scrivener Manuscript or Draft: A Binder folder, identified by a distinctive icon, containing everything Compile can, um … compile. If it’s not in the manuscript/draft, you can’t Compile it. Also, A PDF, image, or ANY hard disk file can become a Scrivener document OUTSIDE the manuscript/Draft, but not INSIDE it.
Scrivener “innards”: the contents (system files and folders) of a .scriv folder or package. They’re hidden inside the package on macOS, but Windows makes it easy to see them, and worse, it forces you to see a few of them at times, notably the .scrivx (XML index file aka Binder). You can open a Windows project by opening the .scrivx, but on macOS, we open the .scriv and never see the .scrivx.
Do not touch. Don’t move or modify project innards unless you know what you’re doing.