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An upgrade from the old EPP package structure (single EPP feature defines the package content) to the new package structure (multiple independent root features in the product define the content) would lead to unintended side effects which are unexpected by most users - one of the most prominent side effect would be the removal of large parts of the content. Because of this it sounds like the best approach to prevent the upgrade from earlier releases (Mars / 4.5) to the new release (Neon / 4.6).
Gerrit change 69371 uses the p2.inf files to prevent updates from versions <= Eclipse Neon M5 in all packages. The p2.inf files are applied to both, the package feature and the product definition: update.id = epp.package.android update.range = [4.6.0.20160301-1200, $version$) update.severity = 0 update.description = Eclipse package upgrade from versions before Eclipse Neon (4.6) is not possible. See bug 332989. I've tested the results with local builds and they seem to work as expected (to everyone else: it is important that the qualifier is incremented, too, in local builds). Nevertheless the solution should be reviewed after Neon M6.
Implemented for all packages with 4.6 M6 (Neon).