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I just did a manual upgrade from 3.9.? (a preview release) to 4.0, and I seem to have lost all the professional features. They are not grayed out, they are simply gone. Also, I notice the outline view always says “no outline available”, no matter what. I’m guessing there are more problems, but I just opened it up.
To get things working well you’ll need to install a fresh instance of Eclipse 3.1 final and MyEclipse 4.0GA. Once that’s done, you can then open your existing workspace and continue development.