I just installed the latest PyDev 4.4.0 plugin to my Eclipse Mars.1. I created a new Java project in a new workspace. And I add the project to a workingset
. In
Well, given that the original report on J2EE is still open: https://bugs.eclipse.org/bugs/show_bug.cgi?id=351764 I don't think this can be fixed at the PyDev side (although it makes the problem appear, it should be fixed on the J2EE side).
As a note, if anyone wants to take a look, on the PyDev side, this happens at: https://github.com/fabioz/Pydev/blob/development/plugins/org.python.pydev/src_navigator/org/python/pydev/navigator/PythonModelProvider.java, but it's done with the proper APIs (using IPipelinedTreeContentProvider), and I'm currently convinced the issue doesn't lie on the PyDev side (although if I'm proved wrong, I'd be happy to fix it).
A workaround would be disabling PyDev or J2EE (depending on which kind of content you use more) just at the explorer level (i.e.: in the explorer do Ctrl+F10, Customize View, Content, disable the PyDev Navigator Content or the Content related to J2EE).