The EpubMerge plugin does not have an ability to add an in-line TOC. Nor am I really interested in adding one.
As enuddleyarbl pointed out, Calibre's built-in ebook Edit feature can insert an in-line TOC in your (merged) EPUB. I did a little bit of testing and found:
- It only puts the TOC at the very front--before the cover, even. But you can move it by just dragging the file in the Edit file browser.
- It uses the existing metadata TOC as source. So if there are nested entries, they will be nested in the in-line TOC. You don't need to worry about all the TOC generation features unless you are editing the metadata TOC.
- You can edit the generated TOC as you like without changing the metadata TOC.
Calibre can also insert an in-line TOC using Calibre Convert from EPUB to EPUB. On the Convert > EPUB Output settings page, there are options to 'Insert TOC' and 'Put inserted TOC at end' instead of beginning. I assume it uses the same code as the Edit TOC insert.
While EpubMerge works very hard to change as little as possible, Calibre Convert re-writes basically
everything. For many (most?) ebooks this is invisible, but it can sometimes cause problems. The only reason to favor inserting TOC with Convert instead of Edit is because you can do it to any number of ebooks at once.