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Currently the end-user should create itself the generation target directory and add it to the build path. This is not the case with the one click generation available from the ecore modeler. Code should be shared between this 2 methods of generation. See http://wiki.eclipse.org/EEF/Tutorials/First_Generation#Generation_and_parameterization
The Eclipse EEF team has worked over the past few months on a brand new runtime using a reflective approach which can be used more easily with Eclipse Sirius. Since we do not plan to continue to work on the old runtime and its code generation approach, I will close this issue for now. If you want to contribute, you can reopen this issue and submit a contribution to the project thanks to our Gerrit: https://git.eclipse.org/r/#/admin/projects/eef/org.eclipse.eef