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Organizing by book is one choice.. but if you want all related things (which may be added through multiple books) in one list (such as Feats or Spells for D&D and Pathfinder), then organizing by book is not as desirable. Indeed.. the Paizo "Pathfinder Reference Document" can be considered one "book" with the contents of multiple volumes in it. While the on-line version is broken out by book.. it is an extra hassle sometimes to need to remember which book a Feat or Spell was introduced in... it is easier to have an alphabetical list of them consolidating all books.
Note: The D&D and Pathfinder spell lists put "Greater X" and "Improved X" spells with the main name (ex. "Lesser Planar Binding" is listed as "Planar Binding, Lesser"). Providing both versions with the "Manage Names" functionality works well until you group them in "A", "B", "C" topics in the navigation hierarchy. Because the aliases all ed up under the parent, "Lesser Planar Binding" is not found under "L", but is under "P" if you put "Planar Binding, Lesser" there .. although it will sort to the top of all the "P" entries.
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