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Reverting back changes from exceptions is necessary to avoid corrupted UI/ core model states in RAM see Bug 346554, which shall implement transaction based updates. The first scenario to tackle is the common file permissions problems which throws IOException. All model element creations and checkin of element modifications must recover from it.
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