Use optional checkboxes to define a filter
Several suggestions on this board involve selecting discontinuous sets of items. An easy way to define these sets would be to (optionally) display a checkbox in front of each tree item. This would allow you to define a persistent set of items for operations such as searching, changing tags or state icons, printing a selected set of items, etc. There are a lot of operations (especially searching and printing) where it would be very useful to define this sort of explicit filter while still being able to see the whole tree.
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mathom
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