fix: respect config defaults when --allowed-mismatches is unset

The change replaces numeric threshold checks with an explicit flag state tracker for the `--allowed-mismatches` option. This ensures per-primer mismatch settings from configuration files are preserved when the CLI parameter is omitted or zero, making the command-line flag act strictly as an explicit override rather than a default fallback.

pkg/obingslibrary/multimatch.go

@@ -777,7 +777,7 @@ func (library *NGSLibrary) ExtractMultiBarcodeSliceWorker(options ...WithOption)
 		library.SetAllowsIndels(true)
 	}
 
-	if opt.AllowedMismatches() > 0 {
+	if opt.AllowedMismatchesIsSet() {
 		library.SetAllowedMismatches(opt.AllowedMismatches())
 	}