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I'll add in some of those punctuations and see if the false positives from them outweigh the false negatives of not having them.
I don't have a problem with it picking up acronyms and other capitalized words. I've got a search to go through the book looking for individual capitalized words so I can check if they should be smallcapped or otherwise formatted. This will just supplement that.
And, as you found in your word processor, I'll still have to manually check every sequence of all-cap words. Calibre doesn't have a Regex -function to Sentence Case things, so I use its Lower Case and its Title Case functions and look for proper names/etc issues to correct. This will just make it easier to find and do the initial conversion.
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