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.

Makefile

@@ -44,13 +44,18 @@ OBITOOLS_DIRS:=$(sort $(patsubst %/,%,$(dir $(OBITOOLS_SRC))))
 OBITOOLS:=$(notdir $(OBITOOLS_DIRS))
 
 
+# Name of the target of a package: its path under pkg/, so that two packages of
+# the same name in different directories (pkg/obialign and
+# pkg/obitools/obialign) do not share a target.
+pkgname=$(subst /,-,$(patsubst pkg/%,%,$(1)))
+
 define MAKE_PKG_RULE
-pkg-$(notdir $(1)): $(1) pkg/obioptions/version.go
-	@echo -n - Building package $(notdir $(1))...
+pkg-$(call pkgname,$(1)): $(1) pkg/obioptions/version.go
+	@echo -n - Building package $(call pkgname,$(1))...
 	@$(GOBUILD) ./$(1) \
-	    2> pkg-$(notdir $(1)).log \
-		|| cat pkg-$(notdir $(1)).log
-	@rm -f pkg-$(notdir $(1)).log
+	    2> pkg-$(call pkgname,$(1)).log \
+		|| cat pkg-$(call pkgname,$(1)).log
+	@rm -f pkg-$(call pkgname,$(1)).log
 	@echo Done.
 endef