How to organize separate client and server repositories for both development and deployment?
A typical workflow in git is to have a development server that uses continuous integration to upload commits as they are made, and then a production server that you manually deploy to with a commit that is deemed "release ready" from the development server.
Having two directories that basically act as a development and production server is an acceptable practice, IMO. You should run the server in production and dev mode at all times, ideally, meaning that you would run dev and prod on different ports.o
More of an opinion than a firm answer, but that's my 2 cents.