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When refactoring package names inside of a module the Manifest file does not reflect the changes made to the the packages. Perhaps this is better posted as a feature request but I feel that this should be the default action. If the packages are re-factored and the Manifest is not updated then the module will not run properly.
It seems that the layer.xml file is also not re-factored.
True, but unlikely to be fixed. apisupport.refactoring has been essentially unmaintained for years. New API features use registration annotations, which do not require any special tool support.
Bug #151116 covers one case. Leaving open for another.
*** This bug has been marked as a duplicate of bug 222788 ***