polish docs references and troubleshooting

[AllanChain]

• Fixes docs source links by setting the docs path for the theme.
• Adds the Read the Docs 404 page extension.
• Redirect to https://jaqmc.readthedocs.io/ for users still using the GitHub Pages site.
• Preserves full field descriptions in generated config references instead of truncating them to the first sentence.
• Replace graphviz workflow illustration with SVG.
• Clarify density defaults and dimensionality.
• Update the troubleshooting page to make it more useful.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.38%. Comparing base (786f080) to head (0281c7c).
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #28   +/-   ##
=======================================
  Coverage   86.38%   86.38%           
=======================================
  Files         125      125           
  Lines        5650     5650           
  Branches      522      522           
=======================================
  Hits         4881     4881           
  Misses        560      560           
  Partials      209      209           

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