Removing old PDF file.

The PDF is being generated on the 'gh-pages' branch, and we do need
to store it here.
Removed changes package; it caused problems.

It seems to mess up formatting of 'emph'.
Additions and moves.

Moved Andreas' new additions to the end of the file instead of the front of the
file.  Added some new refs.
Lots of edits + merged Andreas' additions.

I did a 2nd pass on most of Martin's additions, as well as added new
material of my own.

W.r.t Andreas' edits and additions, I kept all small edits, merged one
of the longer ones, and left a couple of others as comments because I
didn't immediately know how to integrate them.