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When a project uses maven-shade-plugin Netbeans flags it with a warning. "Resolve project problems" reads: "When the final artifact jar contains classes not originating in current project, NetBeans internal compiler cannot use the sources of the project for compilation. Then changes done in project's source code only appears in depending projects when project is recompiled. Also applies to features like Refactoring which will not be able to find usages in depending projects." In my case, the project using maven-shade-plugin is the final application. It has no dependent projects (and never will) and as such these warnings do not apply. Please provide a mechanism to suppress this warning, ideally through the GUI. Ideally, some sort of flag/property should be inserted into the pom.xml file so this suppression is visible to other developers and can be reversed in the future.
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
Still relevant in dev build 201607060002.