@kovid
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1) It is deliberate, there is too much segmentation if you use the full toc tree. One then has to drill down through multiple sections to get to the actual highlight.
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Could it be an option to toggle on/off? I don't think I would mind having to drill down, we already do so in the actual TOC and in the Authors, Tags, etc... panes in the main window.
In fact, as can be seen in the screenshot below, the Search in Book function has results segmented down to at least 3 levels, but they aren't nested. It simply displays with all expanded. I'd love to see the same for highlights, except nested (and perhaps nested as well for Search in Book).
A further suggestion: Perhaps even have an expand/collapse all button in each pane?
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3) I dont see what's special about the highlights list. All tree views in calibre are like this. Adjusting individual trees by a pixel or two is just a recipe for chaos.
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Where else is there a narrowly spaced list like this? As can be seen in the screenshot above, the TOC and Search Results panes have nearly double-spacing. So, I'd actually modify my original request from a couple pixels to 10+, or whatever is used in those panes - they're MUCH easier to read than the Highlights Pane.
I've even just discovered two different features to change spacing in between rows in the book list and tag browser!
So, perhaps the solution is what it has been for most of the annotation features - make it user customizable, like above?