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Beside being cleaner, this would probably help in restructuring Sirius itself in the future, by allowing moving packages in different bundles. The change should concern both internal dependencies between Sirius bundles and from Sirius to other projects. Note that some projects do not version their packages (e.g. SWT) so applying this rule to them would create a lot of warnings for un-versioned dependencies. Either we should propose the projects in question to add versions to their packages, or we should stick to Require-Bundle for them, as long as they represent the exception and are stable projects.
I could not find an automated procedure to do this, so it would be rather costly. In addition, there is a risk that the way we manage version numbers in packages would expose us to potential issues. Maybe we can start with some non-critical plug-ins in 6.0 to gain some experience and see if it's worth the effort.