Thinking about multiple course development, would you need to archive out the current course folder you build to i.e. course_1.zip before starting on another course as the target is always the 'course' folder.
Or, to allow for concurrent course creation (I've never found the time to do one thing at a time myself) could you target the specific course folder say you had a folder named course_healthAndSafety and one called course_UsingAnLMSforNumpties
If that makes sense...