Glad to hear it is now running
Thumbnails are only generated (and saved) if not already present, so subsequent runs should be faster unless you change the thumbnail size setting.
In terms of the time, you should see what the early test releases took! I have around 10,000 books in my library AND I run off a NAS which slows down file access so a lot of work went into removing any redundant I/O to help with performance. This produced an order of magnitude improvement but a run can still take a few hours so you can imagine what performance was like originally (and why I had an incentive to look at how it could Be improved
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If you get an error again trying the rungui.cmd file I would be interested to know what it is to see if the cause can be tracked down and eliminated. The most obvious reason would be not having Java installed, but I am guessing that in this case that was not the cause?