Improved display of generated PDF

Set the title and author fields of PDF and fixed PDF bookmarks to
display all the heading levels I use (by including them in the global
table of contents). Also set links to not be surrounded by distracting
boxes but to be called out by being different colors instead. I may
want to make this color dark blue so it doesn't interfere with
printing.
Changed link color for printing

Changed link color to dark blue so that it would look more like black
when printed in black-and-white. I'll still need to change it if I
want to print a book (to avoid several hundred color printed pages but
still have the figures show up in color)
Promoted overview section to subsection

(Also renamed and promoted the Skip-gram Equation subsections)
New project file