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Not very much anymore.
As for your specific requests:
You can use Calibre's Convert epub->epub or Edit book (under Tools) to inject an in-line ToC. And if you're converting to AZW3 for Kindle, the ToC at the end of the book.
EpubMerge doesn't actually look inside the book contents at all, it only reads/writes the metadata. And nothing says chapter headings inside have to match what the ToC says, or have any consistent formatting to find. So annotating chapter headings is non-trivial.
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