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When you have created a lib directory in your <project>/web/WEB-INF and put some JAR files in it, NB will put these JARs in the project's libraries. Right-click on your project, select properties|libraries. When you have also libraries assigned to your project (through the same project's properties setting) and these libraries encompass one or more of the JARs you put in <project>/web/WEB-INF/lib you will get duplicates in your libraries settings. For libraries that are defined by a project's distributables, that is not an issue perse, but in my opinion NB should identify duplicate libraries. I've already run into errors in my project relating to unresolved library definitions in the past. Iwan
It is not so common use case to have 2 libraries of the same name when 1 is packaged and the second one is not. Or did I miss anything?
I think that people moving from any other environment than NB41 might have WEB-INF/lib defined and filled with relevant JARs, once they discover the benefits of libraries they're likely to miss that they need to delete the duplicates in WEB-INF/lib. In addition I can envision that one would put newer (or older) version of a jar in WEB-INF/lib so that you won't need to define a whole new library for each and every version of a library.
I'm testing this on IDE Dev (Build 071004) and jars from your_project/web/WEB-INF/lib are not automatically added to NB Project Libraries so I guess that resolves this issue.