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[codex] establish three-layer canon and archive superseded public surfaces#2

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sergeeey wants to merge 92 commits into
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feature/mechanistic-taxonomy
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[codex] establish three-layer canon and archive superseded public surfaces#2
sergeeey wants to merge 92 commits into
mainfrom
feature/mechanistic-taxonomy

fix(ci): repair gitleaks checkout depth and restore coverage gate

b3d6dc0
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