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Headless PDE/BUild and Tycho allow creation of nested jars for a bundle, by honouring the source.<jar> and jar.compile.order properties. However, when developing a plugin in IDE, those properties are ignored by incremental build, and that can lead to inconsistencies between IDE and build tools. PDE incremental build in IDE should read properties from build.properties and create nested jars when it makes sense.
Currently we are not actively enhancing PDE build anymore. Therefore, I close this bug as WONTFIX. Please reopen, if you plan to provide a fix.