Welcome to the Community 
I’m afraid you can’t run multiple scans in a single project. You can use the Scanner for .NET that will pick up anything referenced by your .NET solution (including JS). Or you can use the generic Scanner which doesn’t support .NET.
Our support for mono repos covers using multiple projects on a single repo see this thread for more info
I’d be interested to learn more about why you think multiple projects is clumsy in your situation?
Thanks
Tom