Change fonts to charter and source code pro

This commit changes the main font in the paper to Bitstream Charter
and changes the monospaced font (where it's used) to Adobe's Source
Code Pro.
Clean and consolidate ignore list
Add 'tryinput' to input graphs only if they exist

This commit adds the \tryinput macro which will \input the file
if it exists, but silently pass if it doesn't. This can make
compiling the pdf file in intermediate steps easier.
Replace unicode with ASCII in bibliography file
Change NAMESPACE formatting for better git
Change LaTeX package loading for better git
Add recursive window simulations for separate appendix
Cache tizk graphs externally

This commit adds LaTeX code to avoid recalculating the Tikz code
for graphs, which speeds up compilation.
Consolodate header LaTeX into its own file

This commit does some bookkeeping and cleans up the input, usepakage
etc commands. It also puts package loading and macro definitions into
a single LaTeX file.