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Setting the property machine_gtk3 is what's needed. Doing it only for gtk.linux as compiling on other platforms is something that needs to be verified by people building on these platforms but AFAIK no one but linux distros use this profile to compile the whole SDK and the natives(.so) files in one go.
Pushed to master http://git.eclipse.org/c/platform/eclipse.platform.swt.binaries.git/commit/?id=f825bd8a31cfd5db146ffd557f77e1df4d5af031