Multiple hierarchies
Done in 0.4
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Russell, thanks for the comment -- we'll have this feature and we'll have two-way synchronization with links.
Please note: dependency graph may not be representable as a structure if an issue has two "parents" (A->B, A->C, B->D, C->D). So if you set up two-way sync between a structure and depends/blocks link type, you may actually lose links that break hierarchy. Would that be acceptable?
You still will be able to set up one-way sync from links to structure (which won't change the links, only read them) - so non-hierarchical dependencies won't show in structure, but they will be retained as links.
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russell.mull commented
This would be fantastically useful, *especially* if it knew how to synchronize this back into Jira links. You could use it to visualize dependencies, for example.