chore: track worktree checkout, lightweight extension staging and wgs manifests

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Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

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sj

2026-08-21 11:49:48 +08:00

co-authored by Claude Opus 5

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apps/cli/run_rnaseq_qc.py.bak_20260813_225803

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