Integrate Design Documents into docs site#114

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slarson wants to merge 70 commits intomasterfrom

integrate-design-documents

Commits on Feb 20, 2026

Add navigation footers, DD cross-links, and fix DD metadata rendering

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Hyperlink all bare DD references across reader-facing pages

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Convert causal loop diagram from code fence to rendered markdown

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Hyperlink all bare DD cross-references within Design Documents

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Add permalink buttons to all section headers

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Fix Design Document era date from 2024 to 2026

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Fix broken list rendering across all docs

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Add Phase and Layer to every DD with links to Phase Roadmap

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Move TL;DR above Quick Action Reference in all DDs

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Hyperlink all publication citations to DOIs and add master References page

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Clarify DD014 viewer stages vs. roadmap phases, fix mangled DD014.x links

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Rewrite roadmap milestones: what you run, what you see, validated against

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Link all bare citations in DD010 to DOIs

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Add concrete Tier 1 electrophysiology datasets to DD010 and references

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Add systematic expression-consistency validation for Tier 1 in DD010

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Add 5 missing DDs to Phase Roadmap: DD008, DD014.1, DD015, DD022, DD023

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Rename viewer to WormSim 2.0, add WormBrowser history and deployment plan

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Render PlantUML diagrams to SVG, add DD022/DD023 to Integration Map

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Simplify Integration Map: cluster DDs, reduce 78 edges to ~20

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Add clickable DD hyperlinks to all SVG diagrams

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DD006: Fix ConnectomeToolbox integration, add functional connectivity validation

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DD010: Add Tier 2b unc-31 validation, ConnectomeToolbox integration

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DD014.1: Add 14 mockup images for canonical rendering views

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Commits on Feb 21, 2026

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Commits on Mar 17, 2026