Tweak subdirectory dependencies in Makefile
Remove cleanup from pdf recipe

The pdf recipe included the command  which destroys all
of the extra files and makes compilation take longer in the future. I've
removed that command to speed things up.
Add dummy macros for monte carlo and applied section

The empirical section and the simulations define a few latex commands; that
will throw errors if we try to generate the pdf before running the sims.
This commit adds default values of [missing] for those macros so that the
pdf will build.