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When refactoring a project (renaming or removing packages) or inserting new packages, exising javadoc make descriptions produced by the javadoc export assistant are not respected (since they are not known to the project infrastructure?). Refactoring such a project on packages included in such make files result in inconsistent make files and javadoc makes. At least a warning to be remembered or a dialog to adjust the make file (not all newly inserted packages might be included into a documentation) would be helpful.
Moving to JDT/UI.
*** This bug has been marked as a duplicate of 37937 ***