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2 issues, if the first one is taken care of, then the second will go away. #1 - You can enter the same jar file (or folder) multiple times, this probably isn't useful to allow. #2 - If you have the same jar (or folder) in your list twice, if you highlight the second reference to the same jar or folder, and click on the remove button, the one that is hightlighted IS NOT removed, the first one is. A good way to test/reproduce is to include the eclipse/plugins/org.apache.ant_1.4.1/ant.jar file again, so it shows up a second time at the end of the list, and then try deleting the one on the bottom of the list.
I have improved this but it is still possible to add duplicates if you add something that was precomputed for the default path. Reason: the urls that are generated differ. The dialog for adding a jar returns a path with a capitalized drive letter. The path from the plugin libraries has a lower case drive letter!
Fixed in AntClasspathContentProvider. Please verify (Luc)
Verified. Please update the build notes (DarinS).