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I don't do so detailed edits. I don't check for errors, I don't clean the code and I don't rename files or css rules. To me all this is not important - I only care about how the book looks on my ereaders, not how nice the code is. The same for TOC - it must be working, and I only edit it if it's not or is incomplete. As I exclusively use epub2, editing the ncx TOC is simple enough with the TOC editor in calibre.
Sometimes I do merge or split files, and I usually delete some of them, but that is done before reading the book.
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