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Currently, issues and folders can be milestones. Whether an item is a milestone is stored as defined by an internal flag in Structure.Gantt. You can turn this flag on and off by clicking the Toggle Milestone button in the toolbar.
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Gantt Configuration allows you to configure set up a separate JIRA field that would store Milestone date for issues. You can use the same field for Milestone Date and for Start or Finish date for tasks. (Note that it's not currently possible to use Due Date field for that, but we intend to support it soon.)
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