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I think for <class-path-extension>s which have a <binary-origin>, the Libraries node should display those JARs in the usual way. Mainly useful currently for library wrapper modules.
Rather enhancement(?). It is a little different case (would have a different popup-menu, should it it be possible to remove them?, ...). Will need its own specification.
Perhaps technically this is an enhancement request, however this does create a UI inconsistency and a usability issue (the user thinks: did I specify this extension correctly? Because if I did, then I'd expect it to be shown in the logical view.) So I can imagine some users would call this a bug.
I'm not working on APISupport anymore. Reassigning to owner of the component, so the issue is not 'forgotten' forever.
http://hg.netbeans.org/core-main/rev/366a607ab789. No special actions added, 'remove' and perhaps 'edit' would be possible (but hand-editing of project.xml is error prone, we probably don't want to encourage that).
Adding/removing entries is tricky - you can change <class-path-extension> but then there may be files in release/ and/or release.* properties to think about too. See issue #66188.