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Sylph integration: graded absence weight, full-reconciliation mode, and strain-level brainstorm - #300

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Sylph integration: graded absence weight, full-reconciliation mode, and strain-level brainstorm#300
wwood wants to merge 1633 commits into
sylph-condense-regime3from
claude/festive-darwin-tfqmoq

docs: add Word methods section for the sylph-integration algorithms

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