This is the complete message:
WARNING [org.netbeans.TopSecurityManager]: use of system property netbeans.home has been obsoleted in favor of InstalledFileLocator/Places at org.netbeans.Clusters.relativeDirsWithHome(Clusters.java:137)
Any idea?
This is a documented bug in Netbeans Platform 7.4:
"Bug 226333 - Prevent warning about use of system property netbeans.user"
The bug is reported fixed in a nightly build in February 2013. However, my team is still seeing this warning despite the fact that we downloaded 7.4 in December 2013 and have applied all subsequent updates. Therefore I think the easiest fix would be to upgrade to version 8.0.
I was going to suggest that you could also download the 7.4 source code and override the appropriate Utils.java class in the Versioning module to apply the fix by Ondrej Vrabec that is documented here. However the class is final, so an upgrade appears to be the only option.