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When building a product with Tycho, two metadata repositories are being created. One contains all the bundles and features, the other one the product IUs. Because of this separation of repositories, the generated product do not have the -startup argument or the --launcher.library. In of itself, this does not represent a real issue since the executable knows where to look for these files, but in case of updates, or downgrades this could lead to some issue since the wrong version of the file in the install could end up being used. In addition to this, it causes problems when you are trying to lay down the files slightly differently (e.g. bundled mac) since the executable won't find the files at the expected place. Because of the separation of repository, the ApplicationLauncherAction needs to look for the launcher jars in the context metadata repository instead of just the results.
*** Bug 314129 has been marked as a duplicate of this bug. ***
Fixed in master.