Thought I had this fixed, not sure why it came back. Had to add
\normalem to template file to force \emph to be italics, which is
the default. Not sure why it has been doing underlining recently.
Changed default sizes of plots, changed the book template for
pdf creation, and lots of minor edits, most changing bold to
italic, and removing italic for emphasis.
I finally learned that the raw cells let you put latex directly
into the output. So now I have the appendix being created without
the [1] %%latex showing up in the output. Also wrote code to parse
the .tex file to make the Preface a chapter without numbering, so it
is now a proper preface, and not "chapter 0".
I have not touched the Windows generation tools, so PDF generation
in Windows is now broken. I don't think I care.
