Here's my take on your situation. Others may feel differently? I like to describe a JMP Project as a container for all the various elements associated with a body of work. The container can hold lots of elements. To name a few, JMP (data tables, journals, applications, dashboards, scripts, platform reports) and non JMP files such a MS (PowerPoint, Excel, Word) and other files like pdf files, jpeg's, etc. So your automation content (scripts or applications) could sit inside the Project. So what you might want to consider is creating your automation elements and THEN including them as content in the project.