Allow ToC to not be at the top

This adds the ability to put the ToC somewhere other than at the top of
the page.  If a div with id "toc-generator" exists, than the ToC is
placed there.
Don't escape underscores and asterisks

Instead of escaping underscores and asterisks, we now require that
entities contains these characters be `backquoted` in the defaults
files.  This has the additional advantage of identifying formulas and
variable names.
Clarify what files to commit

The documentation markdown files are now generated from the *.defaults
files server-side at publication time.  There is no need to track them.