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I tried ant/project/eg/brokenproj and fixed three problems (all but Java platform; it gave me an NPE, filed separately). Seems to have worked for the most part, but I noticed that at least a change to project.properties (setting a relative path to a subproject) was not saved to disk. I had to go into the project properties dialog and click OK to ensure the change was written to disk. Missing a call to ProjectManager.saveProject somewhere I think. Also be careful that this dialog is not open at the same time as the properties dialog, or they could clash (one could clobber the other).
I did not know I have to explicitely save project. And I also did not update properties under write lock what was clearly mistake. Fixed: src/org/netbeans/modules/java/project/BrokenReferencesModel.java new revision: 1.2; previous revision: 1.1 Re. NPE in platform: I guess it was problem in java/platform otherwise you would file it against me. Re. not opening ResolveConfigurationProblems dialog at the same time as Project Properties: I could disable RCP action when PP is visible, but I'm not sure users would understand it. RCP is modal so vice versa scenario is not possible. Generally I would say that it is problem of PP. If it can be open as modeless dialog than it must expect that there might be external changes - e.g. RCP but more generally user can modify project.properties file, etc.