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041019 custom, JDK 1.5.0. No idea what the cause is.
Created attachment 18414 [details] Stack traces
The "Deletion stacktrace.." runtime exceptions are just informational. They are printed to the console whenever some code accesses an invalid object. This was added to help us to track reasons for InvalidObjectExceptions. In case of FixAllImports tool it seems that InvalidObjectException is properly handled (that's why it is not logged), but the deletion stacktrace remains printed out to the console (because the code that prints it out is not able to determine whether the IOE will or will not be handled properly). To avoid it, the FixAllImports implementation should check whether an object is valid (using isValid) rather than optimistically calling methods on it and handling InvalidObjectException. Anyway, both cases should work fine, so this does not seem to be a bug. Besides these stacktraces I've also found a bunch of NPEs which looks like parser returned a weird AST. I will look at it.
old target milestone, please re-evaluate
Does not seem to be reproducible anymore. We have fixed the deletion stacktraces and the source hierarchy now checks the validity of elements correctly.
Reorganization of java component