I'm not sure I completely follow so bear with me. 
Instead of the repo I currently have that contains only flows.json, flows_cread.json, and package.json, I need to recreate the repo with everything but the files and folders you specified in .gitignore? Once I clone the repo, run npm install and everything should be good.
Then whenever I make changes, I just need to drop into cli to commit the changes and push them to Github?
Copyright OpenJS Foundation and Node-RED contributors. All rights reserved. The OpenJS Foundation has registered trademarks and uses trademarks. For a list of trademarks of the OpenJS Foundation, please see our Trademark Policy and Trademark List. Trademarks and logos not indicated on the list of OpenJS Foundation trademarks are trademarksā¢ or registeredĀ® trademarks of their respective holders. Use of them does not imply any affiliation with or endorsement by them.
The OpenJS Foundation | Terms of Use | Privacy Policy | OpenJS Foundation Bylaws | Trademark Policy | Trademark List | Cookie Policy