Fix dependency loop and update README

Updates the README to clarify installation and running steps. Adds a few steps that were missing or I think could help clarify instructions.

Fixes #21 ~~even though Managed VMs still don't deploy correctly, I will open a separate issue for what I see now.~~ Edit: Got it to work. I've updated the README to clarify that the application will be available at `http://1.$PROJECT_ID.appspot.com` rather than `http://$PROJECT_ID.appspot.com`

Also removed the dependency of `"gcloud-node-todos": "*"` in the cli because this results in a infinite-loop of node_modules that deploying to managed vms isn't smart enough to detect.
If you do this, you shouldn't need to run setup-managed-vms
/cc @ktintc