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When refactoring a project (renaming or removing packages) or inserting new packages, exising jar export descriptions produced by the jar 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 jar 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 the target jar) would be helpful.
This issue will be solved with the upcoming processor/participant architecture.
*** This bug has been marked as a duplicate of 37937 ***