With Eclipse Oxygen (4.7.1a), it is no longer necessary to generate the Eclipse project files, since the Gradle plugin is built-in. The core and desktop projects imported without a hitch, building on the first try.
However, trying to run the desktop app launch configuration threw an exception:
java.lang.NoClassDefFoundError: apple/awt/CGraphicsDevice
A quick Google search for that string revealed this Jogamp forum thread, which proved to be correct.
After removing the Java3d and JAI libraries from /System/Library/Java/Extensions, it worked fine.
My guess is that the Eclipse installer re-introduced these extensions, since I have set them aside many times.