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Okay, so as I want my project to compile out-of-box when pulling out of svn, I like to have a dedicated lib folder. So let's say I need x.jar as my code depends on it, so I add that jar to my dependencies, and it copies it to my own lib/ folder. So far so good. But when I delete x.jar from my dependencies, it does not get deleted from the physical lib/ folder. This can cause stale, never-used jars present in a version-controller project.
The removal of the jar is problematic as the lib folder may be shared by more projects. The only save point where the jar can be removed is when you delete the library from local (folder) storage in library manager.
An idea could be a dialog that asks whether the lib should be physically removed or not (same as "delete project"). I am also against simply deleting libs from the folder when I remove them from the classpath.
This old bug may not be relevant anymore. If you can still reproduce it in 8.2 development builds please reopen this issue. Thanks for your cooperation, NetBeans IDE 8.2 Release Boss