Rename Setup.in to Setup.dist, and assume that configure will create
Setup (instead of creating it from the Makefile).
diff --git a/Modules/Makefile.pre.in b/Modules/Makefile.pre.in
index 6708686..fa94956 100644
--- a/Modules/Makefile.pre.in
+++ b/Modules/Makefile.pre.in
@@ -160,16 +160,12 @@
 		    fi; \
 		done
 
-Setup:		$(srcdir)/Setup.in
-		@if [ -f Setup ] ; then \
-		    echo; \
-		    echo "----------------------------------------------"; \
-		    echo "Modules/Setup.in is newer than Modules/Setup;"; \
-		    echo "check to make sure you have all the updates"; \
-		    echo "you need in your Setup file."; \
-		    echo "----------------------------------------------"; \
-		    echo; \
-		else (set -x; cp $(srcdir)/Setup.in Setup); fi
+Setup:		$(srcdir)/Setup.dist
+		echo "-----------------------------------------------"; \
+		echo "Modules/Setup.dist is newer than Modules/Setup;"; \
+		echo "check to make sure you have all the updates you"; \
+		echo "need in your Modules/Setup file."; \
+		echo "-----------------------------------------------";
 
 
 Setup.local:
diff --git a/Modules/Setup.in b/Modules/Setup.dist
similarity index 98%
rename from Modules/Setup.in
rename to Modules/Setup.dist
index ca83fab..d4be06b 100644
--- a/Modules/Setup.in
+++ b/Modules/Setup.dist
@@ -2,12 +2,12 @@
 # The file Setup is used by the makesetup script to construct the files
 # Makefile and config.c, from Makefile.pre and config.c.in,
 # respectively.  The file Setup itself is initially copied from
-# Setup.in; once it exists it will not be overwritten, so you can edit
+# Setup.dist; once it exists it will not be overwritten, so you can edit
 # Setup to your heart's content.  Note that Makefile.pre is created
 # from Makefile.pre.in by the toplevel configure script.
 
 # (VPATH notes: Setup and Makefile.pre are in the build directory, as
-# are Makefile and config.c; the *.in files are in the source
+# are Makefile and config.c; the *.in and *.dist files are in the source
 # directory.)
 
 # Each line in this file describes one or more optional modules.
diff --git a/Modules/makesetup b/Modules/makesetup
index 0a2794e..09ab50c 100755
--- a/Modules/makesetup
+++ b/Modules/makesetup
@@ -16,7 +16,7 @@
 # Setup files after a -n option are used for their variables, modules
 # and libraries but not for their .o files.
 #
-# See Setup.in for a description of the format of the Setup file.
+# See Setup.dist for a description of the format of the Setup file.
 #
 # The following edits are made:
 #