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1) Open the project explorer view. 2) Create a text file in the workspace. 3) Programmatically add a problem marker to the text file. I did so by executing the following code: IFile file = ResourcesPlugin.getWorkspace().getRoot().getFile(new Path("/MyProject/MyFile")); try { IMarker marker = file.createMarker(IMarker.PROBLEM); marker.setAttribute(IMarker.SEVERITY, IMarker.SEVERITY_ERROR); marker.setAttribute(IMarker.MESSAGE, "test"); } catch (CoreException e) {} 4) Notice in the project explorer view the project has a red X next to it, but not the file. 5) Close the project explorer view and reopen it. Notice the file now has a red X next to it. The file should always have the red X too. This might be related to bug 147467. This is a much simplier example tho.
*** This bug has been marked as a duplicate of 147467 ***