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For what it's worth, given the complexity that the suggested changes would require and the likely bugs that would be almost inevitable, I would prefer that EpubMerge be maintained as a simple tool instead of trying to add in functionality that calibre and it's plugins already offer.
As for the series name? When I merge books from a series into an omnibus, I use the same series name with the series index set to <first book series index>.<last book series index> so if I merge the first 8 books of a series, the series name would be the same and the series index would be 1.08 while books 9 to 16 would have the series index set to 9.16, etc.
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