Already reported before on the project.libraries, but no way how to reproduce so I've added only logging.
Now I've got to the same situation while running under debugger.
So here is a description:
When creating a new per project library an AE is thrown: Creating library in unknown area: ProjectLibraryArea[/Users/tom/NetBeansProjects/JavaApplication1/lib/nblibraries.properties] known areas:  created:  known areas after reinit:  providers: [ProjectLibraryProvider]
The reason is that the ProjectLibraryProvider.getOpenAreas() asks the OpenProjects.getOpenProjects() for list of projects and the then it tries to get the APH by calling AntBasedProjectFactorySingleton.getHelperFor(p). The AntBasedProjectFactorySingleton.getHelperFor just lookups the APH in WeakHashMap<Project,Reference<APH>>.
While the map is OK and contains mapping J2SEProject to APH the OpenProjects returned no J2SEProject but FeatureProjectFactory$FeatureNonProject which does not equal to J2SEProject, so no APH is returned.
Also the OpenProjects.getDefault().openProjects().isDone() returns true.
Fixed jet-main e80b7588f062
Integrated into 'main-golden'
User: Tomas Zezula <email@example.com>
Log: #199458:Projects libraries are broken due to OpenProjects.getOpenProjects() returning FeatureProjectFactory$FeatureNonProject