Symlink problem

[guest73]

My root project folder is a symlink to another folder. In Netbeans I open it through the link.
When I use Get Issue With Sonar Runner I get the following warnings

File '{realPath}/MyFile.java' is ignored. It is not located in module basedir '{linkPath}'.

and nothing is generated.
With the same sonar-project.properties file, however, when I just run ./sonar-scanner from my Linux bash shell from a project root everything works great, so it seems a plugin issue.