inconsistent section numbering

[gregcaporaso]

The notebook and static HTML builds have inconsistent numbering of sections across the TOCs (e.g., click into one of the number sections in the static HTML, and you'll see that the TOC in the section you clicked into has letters instead of numbers. Examples below. We want to have these numbered at all times (e.g., 1.2.3.4, 2.1.3.5, ...).