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Can the tool have a section that displays the accumulated bonuses from the tree?

If you pull down the menu, there should be a label at the bottom left that says "Stats" and one on the bottom-right that says "Builds". Those should transition you between the two views. The stats view is still a bit unorganized, but it's better than nothing.

Could they at least be displayed alphabetically by the bonus? For instance all my "increased accuracy" nodes could be listed at the top?

Or, what could also be fun (but probably a lot harder to code), list the most sought-after stats at the top. For instance, life %, physical (cold/fire/lightning) %, armor/evasion/energy shield increase % (and flat increase). Again, probably difficult to code, but most builds and certainly every hardcore build has certain benchmarks they have to meet in order to not get one shot in red maps/ubers.