I'm in the early stages of a web application that will contain a client side JavaScript application that is deployed to the client's browser and a server side REST type API that will reside on my server. The two will communicate using Ajax and JSON data.
Now here's the thing; they are being developed completely separately, not even sharing one line of code or one resource. Both are Node.js applications. The server side uses express and sequelize for all the server side stuff, and the client side is developed using hem development server with stylus and coffee-script and will be compiled down to 3 files (index.html, application.js and application.css) that will ultimately be deployed by the server as static data.
The part I'm uncertain about it how to version control this. Should they have shared or separate version numbers for instance. Also how should the Git repo look. Is it common for a Git repo root folder to contain two or more folders with separate but intimately related projects? Or should I separate them by branches, one called server, one called client? Or should I split them into two separate repositories altogether? (This would be more expensive as I'm using GitHub private repos)
I'm not looking for anybody to tell me what to do, but inform me of the pros and cons of the alternatives. In your experience what would be the best course of action and why.