Fix nauty interface bug + add more documentation

[kris-brown]

A bug popped up in running Nauty on the arrow category for graphs, which led to cleaning up some of the code (which addressed the bug) and adding better documentation.

This addresses a separate bug for schemas with loops (e.g. DDS): a unique filter was needed when adding the $\phi_{dom}$ and $\phi_{codom}$ edges to the simple undirected graph representation of the ACSet.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.83%. Comparing base (6407367) to head (40f0c47).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #143      +/-   ##
==========================================
+ Coverage   91.61%   91.83%   +0.22%     
==========================================
  Files          23       23              
  Lines        2098     2106       +8     
==========================================
+ Hits         1922     1934      +12     
+ Misses        176      172       -4     

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[kris-brown]

I merged this since it was pretty benign (only interacts with the nauty code which is as of yet unused by general public, merely adds documentation + a tiny bugfix)