Welcome to the Jazz Community Forum
How to set working copy folder on local PC and override files to SCM with Plain Java API?

One answer

This explains how this works in general: https://rsjazz.wordpress.com/2013/10/15/extracting-an-archive-into-jazz-scm-using-the-plain-java-client-libraries/
If you have conflicts on delivery, I don't have an idea how to solve that. You likely have to do a compare first, get a list of conflicts and then to resolve it with your file. Maybe looking at the merge editor in Eclipse can provide you with an idea.