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If you have an aspectj/java application run configuration for a project which no longer exists and you select this configuration from the list of possibilities in the left hand pane of the Run wizard, an error dialog appears. An entry is also placed in the log saying that the project doesn't exist. If you do the same for a java application then no error dialog appears and you just get a message at the top of the configuration saying that the project doesn't exist. The apply, reset and run buttons are also greyed out.
This was fixed under bug 134692