Fix example/figure directory problems
Fix a few compilation errors

All chapters except 3, 4 and 6 compile on their own. Chapters 3 and 6
have issues with skmath (expected to be solved whenever I update skrapport),
and chapter 4 has some obscure issue with the minted environment which I
will have to look into a bit. Nothing caused by the conversion to LaTeX3
as far as I can tell.

Closes #26.