you should be able to edit the endorsed libs setup on the launch configuration available via the server editor.
I open the launch configuration:
I go to tab Arguments:
The right path was already there in "VM Arguments":
"-Djava.endorsed.dirs=C:\boss-6.1.0-SNAPSHOT\lib\endorsed"
I go to tab "Classpath":
Should I also go to tab "Classpath" and add the endorsed libs to the category "User Entries" ?
(Here I cannot find any endorsed libs which was added to the classpath.)