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On a "par" project, I can "Add OSGi bundle nature", but not remove it again. I don't necessarily need to have this option - actually I'm just looking for a way to "enable or disable" the handling of my par projects through the Tooling. My workaround is to fiddle around in the .project file and remove the org.eclipse.wst.common.project.facet.core.builder builder section as well as org.eclipse.wst.common.project.facet.core.nature nature. (moved here from: https://issuetracker.springsource.com/browse/STS-326)
This defect does not seem to exist anymore or at least I cannot reproduce it. I created a new PAR project using the Virgo Tools (current snapshot) and the action "Add OSGi bundle nature" does not show up in the context menu. It is therefore not possible to add the bundle nature to a PAR project from the UI. This is because the mentioned action is declared in plugin.xml with an enablement condition which requires the selected project to neither be a PAR project nor a BUNDLE project, see http://git.eclipse.org/c/virgo/org.eclipse.virgo.ide.git/tree/org.eclipse.virgo.ide.ui/plugin.xml?id=054b216c1672be51834d9b5c646af75127ee5eae#n79 According to git, that enablement condition has been there unchanged since the very first commit with message "initial contribution" dated 2011-03-29. And while this bugzilla entry appears to be newer than the "initial contribution" date, it is actually a copy of STS-326 which is dated 2008-07-02. Given that I cannot reproduce the problem and that the enablement condition seems correctly defined to prevent this issue, I suppose that the problem has been indirectly resolved years ago when the code was moved to Eclipse.org. As such I propose to close the defect as cannot reproduce.
Thanks for investigating this issue. Closing it as suggested by GianMaria in https://bugs.eclipse.org/bugs/show_bug.cgi?id=342583#c1.