[kierandidi]

Fix Sphinx warnings separately from the AtomWorks 3.0 release setup in #114.

• Repair headings, links and docstring markup while preserving explanations and examples.
• Remove duplicate API rendering, unsupported favicon configuration and stale generated timing data.
• Make make html fail on warnings; no executable source changes.
• Validation: clean strict docs builds pass alone and combined with release: prepare AtomWorks 3.0 #114; Ruff and source AST checks pass.