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I must confess that I don't fully comprehend what you are requesting or the specifics on how it would be implemented. I get the idea of a filtered tree that only contains flagged items, and any intervening non-flagged items (which are included in order for all flagged items to be visible [although this would be a departure from the current functionality to *hide* flagged items, and it would entail having to traverse the entire tree to determine what to populate, and UR works hard to minimize how much of the DB it has to read in order to populate the tree, so performance would suffer]), but I'm not clear on how the search results would show a tree structure in like fashion, or if that's even what you're asking (maybe your idea is a new mode for the related items pane that displays [fill in the blank]). If you could elaborate with some examples and pictures or diagrams, it might help. Thanks.
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