Snapshot is a very useful feature. Is it possible to a single snapshot of the entire project or document, including structure, notes, etc? Do the individual file snapshots include notes and keywords?

In a way, yes. In the Snapshot menu, you’ll see two other options in addition to Snapshot for the current document. You can take snapshots of everything you’ve selected in the Binder, or every single document (except for those where Snapshot is not applicable, like media).

This doesn’t take a snapshot of your project, just all of the documents in it. If you want to save the project in its current state, then I suggest using the backup feature in the File menu.

And you can use the Duplicate feature, too, of course (cmd-D), on the Draft folder, which will take a copy of the structure and contents of your Draft folder at any one time.

I forgot to address that question: No, they only capture the current text of a document. Index card, notes, references, keywords, status – all of that is not part of the Snapshot. If you want to save the entire state of a document, then as Keith suggests, Duplicate is the best function for that, and the quickest way to get a complete image of your draft in one shot.