I'm using IDEA 2016.1.3, but I've been running into similar issues from IDEA 15 and on.
Every time we do a Maven install there's an artifact created using the sources plugin called <artifact-name-version>-sources.jar.
When I debug server deployed code, IDEA takes that artifact to debug (step) from the M2 repo instead of my actual class in my IDE. I would prefer to use my actual codebase instead of Maven artifact sources. I can't seem to find a way to get this done.
I asked about something similar some time ago:
So I disabled the choice dialog as I don't want to be choosing a file every time I debug. It's time wasting, irritating and it gets me out of my thought flow.