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Well, I just discovered that my indexing problem was user error, but I will comment about it since it points out an interesting UI issue.
When I bring up the options window, the list of formats shows all the formats with a grey background and it says "index book formats:" When I clicked on 'epub', the epub line was now highlighted with a white background, and the rest of the formats were highlighted in green. I wondered about this, but assumed that I had just selected epub as the format to process.
I was wrong. All formats are apparently selected to be processed by default and I had deselected epub while leaving all other formats selected.
The UI here leaves a bit to be desired for me. First, it is disconcerting that the highlight colors change from grey to green if I click to select a format, or if I simply click to scroll the view. I don't know what this means. Specifically, I didn't realize that all formats were selected (and highlighted, first in grey, then in green) by default. When I click to select a format, the highlight changes, so I assume I have selected that format.
I did not realize I was deselecting formats instead of selecting them. Maybe a checkbox would be more effective in communicating selection than a highlight, especially since the highlight changes colors.
Anyway, once I understood this, cleared all formats, and then selected epub, everything worked fine. On my machine it took less than five minutes to index the library, and search are essentially instantaneous. Nice!
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