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Also does calibre properly test all files to be merged to check if well-formed *before* starting the merge and giving you a chance to abort before the merge? Does it check for duplicate or missing url fragments in all files and give you a chance to abort before starting the merge?
Right now Sigil is checking for well-formed before, during, and after which seems to be a bit of overkill since testing just before should be enough. That should make for a simple speedup.
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