Hi,
Since several of your configurations use target paths, I’m assuming you’re building with Maven. You should then analyze with Maven as well. The benefit is that it handles most of this configuration for you and -by default- passes all the right locations.
In fact, your problem seems to be caused by misconfiguration. For instance, you’ve used both sonar.binaries (long-since deprecated) and synonym/replacement sonar.java.binaries, and you’ve pointed them to different places.
Ann