Phase 1: Disjoint grouping core implementation#341

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s-canchi wants to merge 8 commits intodisjoint-groupingfrom

001-disjoint-grouping

Commits on Mar 11, 2026

add disjoint-group and assemble-groups subcommand scaffolding

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add core grouping, manifest, and validation functions for disjoint grouping

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implement disjoint-group and assemble-groups handlers with --disjoint-dir arg

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add assembly merge and validation, flip to --no-merge-output for scale

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add auto-trigger SW annotation for disjoint-group (T016)

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fix assembly merge and add disjoint-group tests with disjointness validation

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add disjoint grouping reference results for paired and unpaired tests (T019)

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fix unpaired data test to use self.datafname and regenerate ref results

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