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Make remove_all_gap_columns linear and fix empty-row misalignment - #124

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DylanCosto wants to merge 3 commits into

DylanCosto:perf-linear-gap-column-removal

Open

Make remove_all_gap_columns linear and fix empty-row misalignment#124
DylanCosto wants to merge 3 commits into
bxlab:mainfrom
DylanCosto:perf-linear-gap-column-removal

Commits on Oct 11, 2026
- Remove all-gap alignment columns without repeated list deletion
  DylanCosto
  committed
  6549f1f
- Compact shared alignment components only once
  DylanCosto
  committed
  5637291
Commits on Oct 15, 2026
- Merge upstream/main into perf-linear-gap-column-removal
  
  nsoranzo
  and
  claude
  committed
  0499c89