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I've been using draw.io's "horizontal tree layout" feature but I'm having an ordering issue after I've inserted the horizontal tree. For example:

In the navigation, I select ArrangeInsertHorizontal tree, then I build my tree as expected and insert into application. Afterwards, I want to edit the tree by inserting another node at one of the top parts, then re-arrange it by selecting all then ArrangeLayoutHorizontal flow, but when I do this the node that I inserted appears at the bottom of the tree instead of where I want it to go.

Is there a way to place the node exactly where I want it to go? How can I properly order them so they will "auto arrange" correctly?

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The flow and tree are different layouts. If your graph is strictly a tree, then layout as a tree, not a flow. The flow is only needed when you have a directed graph, just not a tree (i.e. each child doesn't have exactly one parent).

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