Can I set all new docs outside of my Manuscript folder to be NOT included in compile?

I want to set up Scrivener so that all new documents are excluded from Compile by default, unless they’re in the Manuscript folder.

Is this possible?

Yes you can.

You will need two things :

A document template that is excluded from compile
A master folder for what is not in your draft.

Then you will select that “Not in draft” master folder, and you will :
image
… and point to your excluded from compile template.

Alternatively, you could simply exclude that master folder from compile, and not bother with the document template.

It’s possible, but why do you want to?

Documents outside the Manuscript folder are essentially invisible to the Compile command. (Unless they’re in the Front Matter folder that you designate, or are explicitly added using the <$include> placeholder.)

“Documents outside the Manuscript folder are essentially invisible to the Compile command.” True. My problem is that some things inside my manuscript folder are NOT included – it was missing about half until I manually set all of the missing items to compile. Is this a bug?

Impossible to say without more information.

For instance, if you recently compiled just one chapter, that would have automatically un-selected everything else.