fix pdf formatting

[ynikitenko]

There are some problems with the pdf version produced by Sphinx or Read the Docs.

• TOC. I could find no way to properly incorporate the manual into the document (it is either in the section "thanks", or I have to include it twice to get a dedicated toc entry).
• formatting. Some strings are formatted incorrectly. This can be due to manual formatting (it is optimised for man). Will anything be improved if we use RST instead of Markdown?
• Release notes. I would add them in a section after Advanced, but could not do it well yet.