Adds a 'Scenario reference' subsection to docs/manual/16-agent-tooling.md: two ruled tables covering every combination of what a directory can hold (only AGENTS.md, only CLAUDE.md, both identical, both different, an inverted mirror, an already-settled symlink) crossed with whether the file is deliberately git-tracked, plus the settled-mirror/later-arrival case separately. Verified against build-manual.py's actual table parser and the generated Starlight site output, not just visual inspection. Also closes the gap this section itself pointed out: nothing previously linked a reader of agents-init.fish or agents-vault.fish's own doc-header to this page, and nothing told a future contributor the page has to be kept in sync. Adds: - CONTRIBUTING.md: a new 'Dedicated manual sections for complex subsystems' subsection documenting the pattern in general (when to use one, and the update-it-in-the-same-change obligation verify-manual.py cannot check for you). - functions/agents-init.fish, functions/agents-vault.fish: a NOTES pointer to the section from each function's own header, so a reader who only sees the header still finds the fuller page.