I go through a sometimes painful process of replacing straight quotes with the correct curly quotes, and marking apostrophes differently from right single quotes (though they render the same), for every book I create. It's not as easy as it might seem at first, especially when there are other issues in the source text, like missing spaces; things like "I heard 'em comin'" are more frequent than one could think.
For ellipses, I choose not to use the single character because: 1) in English I believe it's "better" to use a series of periods separated with non-breaking spaces, and 2) in other languages ellipses should actually look like three periods in a row, so I think it's better to code them like that as well.
Ligatures are a typesetting fancy which should be done by the rendering program, and not coded in the source, like kerning and paragraph breaking. Besides, ligatures whould mess text-search.
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