Help Cloning IonicFramework App from Github Repo

Here is my problem:

I have been working on an app using the IonicFramework for about two weeks and have a friend who wants to help. How do I set him up with the repository and initalize cordova/ionic without deleting any necessary files.

What keeps happening is that I try to install ionic or cordova into the cloned repo and the default tools delete every folder from the repo. When I try to do it the other way around the cordova files are removed.

Anybody know how to deal with this? its ridiculously tedious.

If anyone is unfortunate enough to follow in my footsteps and end up on this thread because of a similar problem as I had, here is a link to a writeup on how i resolved my problem: Ionic Framework, Github, and Multiple Developers