Phase 2 — Port RedundantAlns + paired anchor iteration

[k1sauce]

Part of #1. Depends on #3 (GroupWalk ordering must be in place).

Scope

BT2's `RedundantAlns` (`vendor/bowtie2/aligner_result.cpp:980`) tracks per-cell `(refid, fw, refoff, read_row)` occupancy and rejects new alignments that overlap previously-seen ones. For ungapped same-position alignments this is equivalent to our (ref_id, ref_off, strand) dedup, but for gapped alignments it differentiates much more finely.

Additionally, BT2's `extendSeedsPaired` (`aligner_sw_driver.cpp:1582-2585`) has an outer iteration structure over anchors that interleaves with mate-find in a specific way. Our `align_pair_jointly` is a simplified approximation.

Deliverables

• `RedundantAlns` struct in `crates/rusttie-align/src/redundant.rs` mirroring `aligner_result.h:1657`. Per-cell occupancy hashset, `overlap(&AlnRes) -> bool` + `add(&AlnRes)` methods.
• Integrate into `paired_descent.rs`: before mate-rescue, check `overlap`; before adding to per-mate lists, check `overlap`.
• Port BT2's exact anchor-iteration structure (mate alternation, didAnchor tracking, the do-while inner loop at `aligner_sw_driver.cpp:2326`).
• Pool-diff diagnostic on Phase 0 sample reads: our pool now matches BT2's pool on those reads.

Exit criterion

• chr22 MAPQ at `--joint-descent --seed-hit-cap 1000 -D 1000` jumps to 97%+.
• If it stays at 94%, something else is structural — we re-plan before Phase 3.

Risks

• `RedundantAlns` is per-mate, but in joint-descent we generate pairs. Need to figure out how the per-mate dedup interacts with pair-pool composition (does an excluded mate alignment mean its (mate, partner) pair is also excluded? Yes per BT2 source, but verify).
• BT2's `extendSeedsPaired` interacts with the alignment cache (`AlignmentCacheIface`). We may or may not need to model that.

Files referenced

• `vendor/bowtie2/aligner_result.h:1657` (RedundantAlns class)
• `vendor/bowtie2/aligner_result.cpp:980-1032` (overlap impl)
• `vendor/bowtie2/aligner_sw_driver.cpp:1582-2585` (extendSeedsPaired)
• `crates/rusttie-align/src/paired_descent.rs` (our impl to refactor)