Convert ebook from PDF or wiki to modern toolset -- 2

I have an ebook that I wrote with dokuwiki and it's PDF generation but it was very limited. I need it converted to something simple and easily tracked in a source code revision system (ie git). Some requirements of the new format: Must - Support syntax highlighting - Support inline images - Have a way to highlight important sections (see PDF for example) - Generate TOC - Be able to output a format for kindle and other mobile formats (conversion is fine) - Be a standard set of tools (ie no custom programs or scripts) Not required but nice to have: - Glossary - Foot note generation - Be Linux command line based The "deliverable" will be zip file containing file(s) of source of new ebook, generation of current ebook, and documentation on how to create a new version.