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Definitely something I will consider for future versions, but it will take some different logic and additional parsing routines. My current parser is pretty "dumb": it deletes/modifies tags as it encounters them. One time through the file and done. IDs/links would need to checked against other files (often all or many) to determine whether or not they were being used. In the case of ids, if would be checking all (x)HTMl, all css, as well as the opf/ncx files for each ID encountered to determine if it was unused or not.
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