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.