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(This issue might be valid also for module install.) If user disabled some module(s) the disabling itself is started on the background what means that user can click some menu items and can get exceptions because menu action is just being removed. It would be better to show some modal dialog (progress dialog if possible) telling user that disabling of modules is in progress and disallowing them to do any operations in IDE for that time. From the discussion it looks that proper implementation of this issue does not make any sense before the IDE threading is solved. Add dependencies accordingly please.
6.0 Plugin Manager does not support live disabling anyway.