diff --git a/configure.ac b/configure.ac
index 888b4151487..bf768441fe3 100644
--- a/configure.ac
+++ b/configure.ac
@@ -5878,6 +5878,12 @@ if test $AUTO_DEPEND = yes; then
      AS_MKDIR_P([$dir/deps])
    done
 fi
+if $gl_gnulib_enabled_scratch_buffer; then
+  AS_MKDIR_P([lib/malloc])
+  if test $AUTO_DEPEND = yes; then
+    AS_MKDIR_P([lib/deps/malloc])
+  fi
+fi
 
 AC_OUTPUT
 
diff --git a/lib/Makefile.in b/lib/Makefile.in
index a280b7a3311..e6b1ae6a9ab 100644
--- a/lib/Makefile.in
+++ b/lib/Makefile.in
@@ -67,7 +67,7 @@ endif
 
 DEPDIR = deps
 ifeq ($(AUTO_DEPEND),yes)
-  DEPFLAGS = -MMD -MF $(DEPDIR)/$(*F).d -MP
+  DEPFLAGS = -MMD -MF $(DEPDIR)/$*.d -MP
   -include $(ALLOBJS:%.o=$(DEPDIR)/%.d)
 else
   DEPFLAGS =
@@ -118,7 +118,7 @@ TAGS: $(ETAGS) $(tagsfiles)
 .PHONY: $(ETAGS) tags
 
 clean:
-	rm -f ./*.[ao] ./*-t \#* $(DEPDIR)/*
+	rm -f ./*.[ao] ./*/*.o ./*-t \#* $(DEPDIR)/*.d $(DEPDIR)/*/*.d
 mostlyclean: clean
 	rm -f $(filter-out %-t,$(MOSTLYCLEANFILES))
 distclean bootstrap-clean: mostlyclean
@@ -127,7 +127,7 @@ distclean bootstrap-clean: mostlyclean
 maintainer-clean: distclean
 	rm -f TAGS gnulib.mk
 extraclean: distclean
-	-rmdir sys 2>/dev/null
+	-rmdir malloc sys 2>/dev/null
 
 .PHONY: mostlyclean clean distclean bootstrap-clean maintainer-clean