Have dh_auto_configure pass arch-independent paths to --libdir and --libexec.

debian/rules

@@ -7,6 +7,11 @@ TMP = $(CURDIR)/debian/$(PACKAGE)
 %:
 	dh $@ --with autoreconf
 
+override_dh_auto_configure:
+	dh_auto_configure -- \
+	   --libdir=\$${prefix}/lib \
+	   --libexecdir=\$${prefix}/lib
+
 override_dh_auto_install:
 	dh_auto_install
 	chmod a-x $(TMP)/usr/lib/backupninja/parseini