I recently learned from Ian Bull about Feature Patch Projects which allow you to patch existing features.
This allowed me to replace my self-written clone of the package explorer with a modified one based on the JDT implementation. The benefit of this approach is that the Mylyn filtering also works which I really missed in my implementation.
The filtered package explorer allows to filter the projects by name as demonstrated in the following screenshot.
I created an update site you that you can try it out. Please note that Eclipse only allow one feature patch per features, so in case you have already something installed which modifies JDT my patch will properly not work. I think STS, AspectJ, Groovy and the like also patch JDT but I’m not sure if they only patch JDT core or also JDT UI.
p2 Update Site:
I also opened a bug to discuss if that feature would be used in the standard JDT Package Explorer: Bug report.
If you want to restore the original package explorer, just use p2 to de-install it again.