@Ronan : We'll make a note to try and fix up the documentation a bit. Hopefully I can answer the rest of your questions:
1. Assuming you are talking about the "Save As" action on an existing Workbook, then yes, all of the files that are contained in the original Workbook are saved in the new Workbook. It's really just a file rename (plus any changes that may have been done since last save of the original document).
2. The Maple Workbook is basically a SQLite database file. All of the attachments are stored inside of this file. For any non-Maple mw files, you should be able to right click on them and go to "Show in folder", which will open the containing folder inside of the Workbook database file. Now there isn't a way to access this from outside of Maple (that I know of), but inside of Maple, you can access Workbook content using the same file / folder structure as is shown in your workbook navigator tree. So say you had an Excel file attached to your Workbook. You should be able to do:
In the above "this:///" represents the root of the Workbook tree. Have a look at ?worksheet,workbook,uri for more detail.
3. This one's easy. It's the first letter of the filename for the Workbook. We added this to give some visual indication that files belong to a given Workbook when you have multiple Workbooks open.
4. Not yet. But revision control is definitely on our radar with the Workbook project.
I hope that covers it. If not, let me know.