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When using the "Viewpoint Specification Project", the MANIFEST.MF file always contains a dependency to org.eclipse.sirius.common.acceleo.mtl, even if the optional support of Acceleo3 is not installed. The Acceleo 3 is currently the default query language. But it is not mandatory, so this dependency should be an option in the wizard. Ideally, the wizard should propose the query language to use (according to those installed) and according to the user choice, the wizard should add the necessary dependencies.
The manifest .mf is created in ViewpointSpecicationProject.convert(), line 352: ViewpointSpecificationProject.createFileFromTemplate(prj, "META-INF/MANIFEST.MF", "resources/MANIFEST.MF", replacements, monitor); //$NON-NLS-1$ $NON-NLS-2$ The template file explicitetly contains the dependency to org.eclipse.sirius.common.acceleo.mtl At the end of the convert() method, the addAcceleoNature() is called. It adds the Acceleo nature only if the Acceleo bridge is present (if the conversion command defined in org.eclipse.sirius.common.acceleo.mtl.ide exists).