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What software do i use to edit the .mobi file?
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You
can't directly edit a mobi file. You have to have the source (epub, (x)html , whatever) properly formatted
before you build the mobi from that source. A mobi is a binary file, so once it's built... all editing (except for metadata) stops. "Editing" a mobi file involves re-building it... either by maintaining the original source somewhere, or by unpacking the mobi - editing - and
then rebuilding.
For the TOC to show up in your Kindle, you need to do two things with your Sigil-built ePub (before converting it to mobi with kindlegen):
1) you need to create an inline (html) representation of your TOC in Sigil—this is what you will SEE on your Kindle when you click "Go To->table of contents." Be sure to right click on the file (in Sigil) that represents your TOC and mark it (Semantics) as "Table of Contents."
Note: this is a manual process. Nothing in Sigil will automatically generate a TOC that will just "appear" on the Kindle when you convert the epub to mobi. You have to
make the HTML Table of Contents yourself.
2) you need create an ncx TOC (external) in Sigil. You can auto-generate the toc.ncx from the Headers (h1, h2, h3) in your book. This will produce the navigation "dots" on the progress bar on the Kindle.
Item 1 may be enough, but unless kindlegen KNOWS where your TOC is in your epub, it can't know where to jump to when clicking "Go to->table of contents."
I've described how you can do this with only the gui tools in Sigil. But with the newest version of Sigil, you can manually do the same things ATDrake described above by directly editing the opf file and the toc.ncx file. Brushing up on the nitty-gritty of hand-building opf files and ncx files will go a long way toward understanding how you can then do it more easily with gui programs.