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There is a project in eclipse.pde repo, where the readme says it has been moved to eclipse.pde.ui repo. It has same name in both, so it makes it hard to "import projects" and get the right one. A person really has to dig to realize they should not import the old one from eclipse.pde. Could probably improve the situation by changing name in .project file (of old one) to "org.eclipse.pde-moved" (or similar) but I believe it can and should just be removed from the "active branch". Its just clutter at this point. I'm assuming the same is true of 4.3 maintenance branch ... but have not explicitly checked.
I've simply removed the .project and .classpath files with http://git.eclipse.org/c/pde/eclipse.pde.git/commit/?id=e09dfa8cb2b41a30fe9855e0ddcedf69a206fb45 > I'm assuming the same is true of 4.3 maintenance branch ... but have not > explicitly checked. We won't touch 4.3.x at this point.
+1, I had the same change in my local repository. If there wasn't a fire alarm forcing an evacuation I would have pushed it :)
Verified in master.