Rename the master file

topdown.tex doesn’t really scream “this is the master file”, and
topdown.pdf is a positively silly name for the final product.

Also update the Makefile to use latexmk.
Fix problem with italic scope

\textit is a LaTeX-style command that takes an argument, rather than
a plain TeX-style command that changes the style for the remainder of
the block.
Remove workarounds for old bugs

Honestly I can’t remember what these bugs exactly were, but it seems
dangerous to leave in patches for old packages that have since been
updated.
Revert to Minion

This document was originally set in Minion. Rather late in the
process, the university introduced a new set of rules governing
the format of a PhD thesis that, bizarrely, mandated the use of
sans serif type. I believe this rule was eventually overturned
following the protests of faculty in the sort of mathematical
disciplines that have never developed the habit of using sans-
serif, but not before I had reformatted the thesis in Myriad.

However I find it a more attractive document in its original
setting, so this seems a reasonable opportunity to revert.
Add PDF files to repository

It would be nice to have the final PDF here, for the benefit
of anyone who does not own the necessary fonts.

In the process of doing this, I realised that the PDF diagrams
from the semicc project had been omitted incorrectly, since
they were caught by the blanket “*.pdf” that I had in .gitignore.
Updated BBL

To reflect the recent change to cs.bib.