feat: add SIMD alignment algorithms

[claymcleod]

omics-alignment had deterministic scalar global and local alignment but no byte-oriented SIMD path for high-throughput sequence comparison. This added adaptive i16/i32 anti-diagonal wavefronts with exact scalar parity, Apple Silicon NEON, runtime-detected Linux AVX2, compact traceback, and scalar fallback for unsupported hardware or score ranges.

Differential tests covered edge cases and fixed-seed workloads on both native backends, while benchmarks and CI added Apple Silicon and Linux coverage. Apple Silicon performance met the acceptance target; AVX2 timing remains provisional until the same benchmark runs on physical AMD64 hardware, although AVX2 correctness and generated hot-loop instructions were verified.

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[github-actions]

Bencher Report

Project	omics
Branch	main
Testbed	github-actions

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Benchmark	Latency	nanoseconds (ns)
algorithms/global/asymmetric/scalar/1024	📈 view plot ⚠️ NO THRESHOLD	20,412,000.00 ns
algorithms/global/asymmetric/scalar/16	📈 view plot ⚠️ NO THRESHOLD	5,357.20 ns
algorithms/global/asymmetric/scalar/256	📈 view plot ⚠️ NO THRESHOLD	1,177,200.00 ns
algorithms/global/asymmetric/scalar/64	📈 view plot ⚠️ NO THRESHOLD	74,430.00 ns
algorithms/global/asymmetric/simd/1024	📈 view plot ⚠️ NO THRESHOLD	1,582,600.00 ns
algorithms/global/asymmetric/simd/16	📈 view plot ⚠️ NO THRESHOLD	4,375.20 ns
algorithms/global/asymmetric/simd/256	📈 view plot ⚠️ NO THRESHOLD	139,390.00 ns
algorithms/global/asymmetric/simd/64	📈 view plot ⚠️ NO THRESHOLD	19,518.00 ns
algorithms/global/balanced/scalar/1024	📈 view plot ⚠️ NO THRESHOLD	40,624,000.00 ns
algorithms/global/balanced/scalar/16	📈 view plot ⚠️ NO THRESHOLD	9,792.20 ns
algorithms/global/balanced/scalar/256	📈 view plot ⚠️ NO THRESHOLD	2,343,100.00 ns
algorithms/global/balanced/scalar/64	📈 view plot ⚠️ NO THRESHOLD	148,820.00 ns
algorithms/global/balanced/simd/1024	📈 view plot ⚠️ NO THRESHOLD	3,223,600.00 ns
algorithms/global/balanced/simd/16	📈 view plot ⚠️ NO THRESHOLD	7,519.40 ns
algorithms/global/balanced/simd/256	📈 view plot ⚠️ NO THRESHOLD	276,370.00 ns
algorithms/global/balanced/simd/64	📈 view plot ⚠️ NO THRESHOLD	36,720.00 ns
algorithms/global/gap-heavy/scalar/1024	📈 view plot ⚠️ NO THRESHOLD	47,873,000.00 ns
algorithms/global/gap-heavy/scalar/16	📈 view plot ⚠️ NO THRESHOLD	12,023.00 ns
algorithms/global/gap-heavy/scalar/256	📈 view plot ⚠️ NO THRESHOLD	2,737,000.00 ns
algorithms/global/gap-heavy/scalar/64	📈 view plot ⚠️ NO THRESHOLD	176,600.00 ns
algorithms/global/gap-heavy/simd/1024	📈 view plot ⚠️ NO THRESHOLD	3,763,900.00 ns
algorithms/global/gap-heavy/simd/16	📈 view plot ⚠️ NO THRESHOLD	7,860.60 ns
algorithms/global/gap-heavy/simd/256	📈 view plot ⚠️ NO THRESHOLD	309,550.00 ns
algorithms/global/gap-heavy/simd/64	📈 view plot ⚠️ NO THRESHOLD	38,903.00 ns
algorithms/local/asymmetric/scalar/1024	📈 view plot ⚠️ NO THRESHOLD	22,405,000.00 ns
algorithms/local/asymmetric/scalar/16	📈 view plot ⚠️ NO THRESHOLD	5,234.00 ns
algorithms/local/asymmetric/scalar/256	📈 view plot ⚠️ NO THRESHOLD	1,268,200.00 ns
algorithms/local/asymmetric/scalar/64	📈 view plot ⚠️ NO THRESHOLD	79,591.00 ns
algorithms/local/asymmetric/simd/1024	📈 view plot ⚠️ NO THRESHOLD	2,336,600.00 ns
algorithms/local/asymmetric/simd/16	📈 view plot ⚠️ NO THRESHOLD	4,573.00 ns
algorithms/local/asymmetric/simd/256	📈 view plot ⚠️ NO THRESHOLD	189,580.00 ns
algorithms/local/asymmetric/simd/64	📈 view plot ⚠️ NO THRESHOLD	22,315.00 ns
algorithms/local/balanced/scalar/1024	📈 view plot ⚠️ NO THRESHOLD	44,677,000.00 ns
algorithms/local/balanced/scalar/16	📈 view plot ⚠️ NO THRESHOLD	10,252.00 ns
algorithms/local/balanced/scalar/256	📈 view plot ⚠️ NO THRESHOLD	2,544,000.00 ns
algorithms/local/balanced/scalar/64	📈 view plot ⚠️ NO THRESHOLD	159,620.00 ns
algorithms/local/balanced/simd/1024	📈 view plot ⚠️ NO THRESHOLD	4,733,400.00 ns
algorithms/local/balanced/simd/16	📈 view plot ⚠️ NO THRESHOLD	8,086.60 ns
algorithms/local/balanced/simd/256	📈 view plot ⚠️ NO THRESHOLD	378,160.00 ns
algorithms/local/balanced/simd/64	📈 view plot ⚠️ NO THRESHOLD	42,740.00 ns
algorithms/local/gap-heavy/scalar/1024	📈 view plot ⚠️ NO THRESHOLD	52,153,000.00 ns
algorithms/local/gap-heavy/scalar/16	📈 view plot ⚠️ NO THRESHOLD	12,637.00 ns
algorithms/local/gap-heavy/scalar/256	📈 view plot ⚠️ NO THRESHOLD	2,980,300.00 ns
algorithms/local/gap-heavy/scalar/64	📈 view plot ⚠️ NO THRESHOLD	189,370.00 ns
algorithms/local/gap-heavy/simd/1024	📈 view plot ⚠️ NO THRESHOLD	5,457,300.00 ns
algorithms/local/gap-heavy/simd/16	📈 view plot ⚠️ NO THRESHOLD	8,253.20 ns
algorithms/local/gap-heavy/simd/256	📈 view plot ⚠️ NO THRESHOLD	422,250.00 ns
algorithms/local/gap-heavy/simd/64	📈 view plot ⚠️ NO THRESHOLD	46,104.00 ns
contig::new	📈 view plot ⚠️ NO THRESHOLD	19.18 ns
coordinates::interbase::try_new	📈 view plot ⚠️ NO THRESHOLD	27.27 ns
intervals::interbase::from_raw_coordinates	📈 view plot ⚠️ NO THRESHOLD	60.07 ns
intervals::interbase::try_new_prepared	📈 view plot ⚠️ NO THRESHOLD	16.37 ns
positions::base::checked_add	📈 view plot ⚠️ NO THRESHOLD	1.76 ns
positions::base::checked_sub	📈 view plot ⚠️ NO THRESHOLD	2.11 ns
positions::base::try_new	📈 view plot ⚠️ NO THRESHOLD	0.35 ns
positions::interbase::checked_add	📈 view plot ⚠️ NO THRESHOLD	0.71 ns
positions::interbase::checked_sub	📈 view plot ⚠️ NO THRESHOLD	0.70 ns
positions::interbase::new	📈 view plot ⚠️ NO THRESHOLD	0.35 ns
structural::classify::deletion	📈 view plot ⚠️ NO THRESHOLD	6.69 ns
structural::classify::insertion	📈 view plot ⚠️ NO THRESHOLD	6.68 ns
structural::classify::interchromosomal_translocation	📈 view plot ⚠️ NO THRESHOLD	5.99 ns
structural::classify::intrachromosomal_translocation	📈 view plot ⚠️ NO THRESHOLD	67.64 ns
structural::classify::inversion	📈 view plot ⚠️ NO THRESHOLD	12.62 ns
structural::classify::tandem_duplication	📈 view plot ⚠️ NO THRESHOLD	5.63 ns
structural::parse::deletion	📈 view plot ⚠️ NO THRESHOLD	444.98 ns
structural::parse::insertion	📈 view plot ⚠️ NO THRESHOLD	858.82 ns
structural::parse::interchromosomal_translocation	📈 view plot ⚠️ NO THRESHOLD	443.60 ns
structural::parse::intrachromosomal_translocation	📈 view plot ⚠️ NO THRESHOLD	1,451.40 ns
structural::parse::inversion	📈 view plot ⚠️ NO THRESHOLD	966.38 ns
structural::parse::tandem_duplication	📈 view plot ⚠️ NO THRESHOLD	561.04 ns
variants::display::insertion_interbase_qualified	📈 view plot ⚠️ NO THRESHOLD	236.00 ns
variants::display::snv_base_qualified	📈 view plot ⚠️ NO THRESHOLD	222.17 ns
variants::intervals::alternate_deletion	📈 view plot ⚠️ NO THRESHOLD	28.25 ns
variants::intervals::alternate_delins	📈 view plot ⚠️ NO THRESHOLD	23.10 ns
variants::intervals::alternate_insertion	📈 view plot ⚠️ NO THRESHOLD	39.89 ns
variants::intervals::reference_deletion	📈 view plot ⚠️ NO THRESHOLD	23.75 ns
variants::intervals::reference_insertion	📈 view plot ⚠️ NO THRESHOLD	10.71 ns
variants::normalize::collapse_to_insertion	📈 view plot ⚠️ NO THRESHOLD	78.62 ns
variants::normalize::trim_to_snv	📈 view plot ⚠️ NO THRESHOLD	83.26 ns
variants::parse::deletion_base_qualified	📈 view plot ⚠️ NO THRESHOLD	391.47 ns
variants::parse::delins_base_qualified	📈 view plot ⚠️ NO THRESHOLD	430.74 ns
variants::parse::insertion_interbase_qualified	📈 view plot ⚠️ NO THRESHOLD	366.83 ns
variants::parse::mnv_base_qualified	📈 view plot ⚠️ NO THRESHOLD	470.30 ns
variants::parse::reject_mismatched_qualifier	📈 view plot ⚠️ NO THRESHOLD	300.49 ns
variants::parse::reject_missing_qualifier	📈 view plot ⚠️ NO THRESHOLD	161.40 ns
variants::parse::snv_base_qualified	📈 view plot ⚠️ NO THRESHOLD	402.86 ns

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