You should not use WinSCP to push code up to your application. You certainly can but you lose out on a lot of the functionality. The proper way to push code to OpenShift is via git.
To answer your question, the application root is located at:
~/app-root/runtime/repo/php/
Let me know your thoughts on the CI quickstart. I wrote in almost 18 months ago and it probably needs an update.
-- gs