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The setting for filtering of subtasks that don't match queries is difficult to discover. Considering the value of the feature it could make sense to enable it by default. To ensure a smooth migration for users with existing Task Lists we could display a message that links to a dialog that explains how to disable the filter to show tasks any tasks that were hidden.
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