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docs(nav): place the eight orphan pages - #34

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What changed

Nine docs pages were built but absent from the nav. Eight now have a place: intro video under Home; David & Nielsen 2005 and the urea-cycle Recon3D map beside the GEM primer; the system coverage layer after events; the seven-systems vocabulary note after notational conventions; Lab 5 (vitamin D vehicle) in the cookbook; the pathway-types refactor and the nutrition ontology spec under Architecture.

The ninth, VMH-LICENCE-ENQUIRY.md, is a draft email with a third party's contact details. It is listed under not_in_nav with a comment saying why, so the strict build stays quiet without pretending it is a reader page. Whether it belongs in a public docs tree at all is a separate question for the maintainer.

Checks I ran locally

  • mkdocs build --strict with no "not included in nav" notice

🤖 Generated with Claude Code

…ut of the nav on purpose

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>

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