While debugging a java app in eclipse I receive a \"Source not found\" error in two cases:
I've had a related issue in connection with Glassfish server debugging in Eclipse. This was brought about by loading the source code from a different repository (changing from SVN to GitHub). In the process, the wrong compiled classes were used by the Glassfish server and hence, the source and run time would be out of sync with break points appearing on empty lines.
To solve this, rename or delete the top folder of the classes directory and Glassfish will recreate the whole class directory tree including updating the class files with the correctly compiled version.
The classes directory is located in: /workspace/glassfish3122eclipsedefaultdomain/eclipseApps/< your Web Application>/WEB-INF/classes