Fix TOC in PDF assembly

[lenkis]

Problem: In all PDF files we have problems with subsections of the 1st section. Instead of staying subsections, they are promoted to the section level. For example, this structure:

1. Section
    1.1. Subsection A
    1.2. Subsection B
2. Section

is represented like this:

1. Section
2. Subsection A
3. Subsection B
4. Section

This affects not only TOC representation. The entire document is assembled with the wrong structure and section numbers.

Known workaround: create an empty file and define it as the first section in toctree.rst.

Reviewer: @lenkis