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The debugger when displaying source code lines in the editor, currently looks up its guess at the Java source file name in the Repository, then finds the data object, gets the LineCookie, etc. Howev er, as it hardcodes the .java extension, this will make it unable to debug any other types of source (e.g. other languages) that compile to bytecode and provide the Elements hierarchy. Suggest that it instead use the new ClassElement.Finder to look up the proper class element that this class comes from. Then get the containing source element. Now try to find the data object providin g this source element--probably the SourceElementImpl in the JDO module should have a DataObject cookie which would return the JDO, I think this would be natural. Then proceed as usual. Or, use RemoteClass.getSourceFileName, although I think this gives only the filename and not package, so you would have to look for that filename in what you guessed was the right folder.
Resolved for 3.3.x or earlier, no new info since then -> closing.