move newcommands to header.tex

This gets us closer to pandoc->epub showdown. The pandoc folks were very responsive and fixed two bugs that I found in the org reader. 

It looks like epub might happen sooner than later. I am still looking into the glossary and the illustrations. I think that using jgm's pandoc-filters python library might make things a breeze to handle the small changes. If only I knew someone that had some python skills;) 

I should have a decent game plan to discuss/present to you by the end of week.