docs: apply AI-generated documentation overhaul from proposals#48
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Steffengreiner wants to merge 5 commits intomainfrom
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docs: apply AI-generated documentation overhaul from proposals#48Steffengreiner wants to merge 5 commits intomainfrom
Steffengreiner wants to merge 5 commits intomainfrom
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Replace all 22 documentation pages and mkdocs.yml with the reviewed proposal versions generated by the multi-agent debate system. Changes include plain-language rewrites across every section, consistent step-by-step formatting, What's next navigation footers, and a restructured nav in mkdocs.yml (workflow order, User account section, Ontology search flattened, Developers & Stewards renamed to Reference).
- Remove docs/proposals/ now that all pages have been merged into the live documentation - Add AGENTS.md documenting the multi-agent debate system - Add opencode.json with agent definitions and permissions
…undancy, and apply nav quick wins - Enforce single forward-facing link in What's Next across all 20 doc pages - Replace concepts.md What's Next with See Also (reference page pattern) - Add inline cross-references: password/profile, collaborator tips, search tips, confounding variable tips, TIB/NCBI info, metadata glossary ref - Replace process lists with mermaid diagrams in measurement_registration and raw_data_download - Consolidate ROR Organisation ID into single note above tabbed sections in measurement_registration - Replace repeated ontology search instructions with tip admonitions linking to canonical page - Update index.md with release notes v1.12.0-v1.12.5 including PI/PM swap action item - mkdocs.yml: wrap Sample batch in Samples section, promote Metadata glossary to top-level, rename Reference to Developer reference, rename Editing to Edit, enable navigation.sections
…ion headers - Split 8-node mermaid workflow into two 4-node diagrams for better readability - Add CSS for navigation.sections headers: uppercase, brand colour, letter-spacing, and subtle bottom border to make sidebar groups visually prominent
…d diagrams - Replace two-row LR layout with single vertical TD flow for better readability - Add CSS to centre all mermaid diagrams on the page
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Summary
outlined in the agents.md file)mkdocs.ymlnav to follow user workflow order, adds a dedicated User account section, flattens Ontology to a single entry, and renames Developers & Stewards → ReferenceWhat changed
docs/index.mddocs/get_started/process_overview.mddocs/user/*docs/project/*docs/experiment/*docs/batch/sample-batch.mddocs/measurement/*docs/rawdata/*docs/ontology_search/*docs/metadata/concepts.mddocs/developers/api.mdmkdocs.ymlReview notes
This PR was generated by the multi-agent documentation debate system described in
AGENTS.md.