Refactor similarity engine and implement parallel clustering

Introduces parallel processing for clustering, refines scoring mechanisms, and expands test coverage for the alignment functionality.

This change introduces parallel processing capabilities within the clustering logic, updates the core similarity engine with new data structures and scoring methods, and implements a comprehensive test suite for the alignment tool. It also adds new command-line options for configuring alignment parameters and reference lengths.

pkg/obisimilarity/block_nosimd.go

@@ -0,0 +1,10 @@
+//go:build !goexperiment.simd
+
+package obisimilarity
+
+// simdBlockWidth is 0 without SIMD: the blocks are not used.
+func simdBlockWidth() int { return 0 }
+
+func blockCommon(data []uint8, width int, words []uint16, out []uint8) {
+	panic("obisimilarity: blocks of tables require GOEXPERIMENT=simd")
+}