Due to structural changes you cannot update from a Mars (or prior) all-in-one package to a Oxygen version. If interested in the technical details, see bug 332989 and bug 490515 and Bug 462282
http://www.eclipse.org/eclipse/news/4.5/platform.php#macapp
https://wiki.eclipse.org/Platform-releng/Issues_related_to_Mac_App_installations
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