Fix Doxygen rendering: use native math syntax and clean up refs

Convert all math delimiters from GitHub markdown dollar signs to
Doxygen native (backslash-f) so that LaTeX commands like dot are
passed verbatim to MathJax instead of being intercepted by Doxygen
command parser (which was interpreting dot as a Graphviz directive
and truncating the page).

Also replace per-section paper citations with a single link to the
papers page and fix bold markers around inline formulas.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson