Clean up and tweak project Makefile

Some targets were being unnecessarily rebuilt; this commit makes a
few changes to the Makefile that should prevent that. In particular,
paper.pdf depended on the appendix's plots and that's been fixed.

After this commit we still sometimes leave the pdf files older than
their dependencies if latexmk doesn't decide to run, but I'm reluctant
to force-update the timestamp for the files. It seems like that's a
case where we should manually run pdflatex just to make sure everything
has been processed.

Fixup last commit
Graphs: fix dimensions of McCracken plots
Monte Carlo: reduce number of simulations

5000 simulations => 60GB database file (which, along with intermediate
files, kills my desk space). Let's drop it down to 2000 simulations.
Styling: tweak spacing and font size

- changes the font to 12pt charter instead of 11pt
- changes the margins to 1.25in instead of 1in
- changes to single spacing instead of 1 and a half spacing.

Hopefully these all make the document easier to read; I'll probably
undo them before submission though.