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When I create a new query all hits are marked as incoming and a notification window pops-up. This does not provide any useful information for me since I explicitly created the query and I'm aware that I have not read any of the tasks. Moreover I can see that I have not downloaded the task due to the missing task data icon so the same information is displayed twice. I suggest that hits for newly created queries are not marked as incoming.
This will require some design discussion, bug 161734 is related.
Mylyn has been restructured, and our issue tracking has moved to GitHub [1]. We are closing ~14K Bugzilla issues to give the new team a fresh start. If you feel that this issue is still relevant, please create a new one on GitHub. [1] https://github.com/orgs/eclipse-mylyn