diff --git a/aclocal.m4 b/aclocal.m4
index 328a345a601..060767aa28d 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -140,7 +140,8 @@ dnl
 dnl Usage: AC_REQUIRE([WINE_CONFIG_HELPERS])
 dnl
 AC_DEFUN([WINE_CONFIG_HELPERS],
-[AC_SUBST(ALL_MAKEFILE_DEPENDS,["# Makefile dependencies"])
+[AC_SUBST(ALL_MAKEFILE_DEPENDS,["# Makefile dependencies
+Makefile: Makefile.in Make.rules config.status"])
 AC_SUBST(ALL_WINETEST_DEPENDS,["# Test binaries"])
 
 AC_SUBST(ALL_MAKERULES,"")
@@ -171,12 +172,16 @@ wine_fn_append_rule ()
 wine_fn_config_makefile ()
 {
     ac_dir=$[1]
-    ac_deps=$[2]
+    ac_enable=$[2]
     wine_fn_append_file ALL_DIRS $ac_dir
     wine_fn_append_rule ALL_MAKEFILE_DEPENDS \
 "$ac_dir/__clean__ $ac_dir/__install__ $ac_dir/__install-dev__ $ac_dir/__install-lib__ $ac_dir/__uninstall__ $ac_dir: $ac_dir/Makefile
-$ac_dir/Makefile $ac_dir/__depend__: $ac_dir/Makefile.in config.status $ac_deps
+$ac_dir/Makefile $ac_dir/__depend__: $ac_dir/Makefile.in config.status Make.rules \$(MAKEDEP)
 	@./config.status --file $ac_dir/Makefile && cd $ac_dir && \$(MAKE) depend"
+    AS_VAR_IF([$ac_enable],[no],,[case $ac_dir in
+                 */*) ;;
+                 *) wine_fn_append_file ALL_TOP_DIRS $ac_dir ;;
+               esac])
 }
 
 wine_fn_config_lib ()
@@ -345,19 +350,12 @@ AC_CONFIG_FILES([$1])])
 
 dnl **** Create a makefile from config.status ****
 dnl
-dnl Usage: WINE_CONFIG_MAKEFILE(file,deps,var,enable)
+dnl Usage: WINE_CONFIG_MAKEFILE(file,enable)
 dnl
 AC_DEFUN([WINE_CONFIG_MAKEFILE],[AC_REQUIRE([WINE_CONFIG_HELPERS])dnl
-m4_pushdef([ac_dir],m4_bpatsubst([$1],[^\(\(.*\)/\)?Makefile$],[\2]))dnl
-m4_pushdef([ac_name],m4_bpatsubst(ac_dir,[.*/\(.*\)$],[\1]))dnl
-m4_if(ac_dir,,WINE_APPEND_RULE(ALL_MAKEFILE_DEPENDS,[$1: $1.in $2 config.status])
-AC_CONFIG_FILES([$1]),
-[wine_fn_config_makefile ac_dir m4_if(ac_dir,tools,[$2],["$2 \$(MAKEDEP)"])
-AS_VAR_PUSHDEF([ac_enable],m4_default([$4],[enable_]ac_name))dnl
-m4_ifval([$3],[test "x$ac_enable" != xno]m4_foreach([ac_var],[$3],[ && WINE_APPEND_FILE(ac_var,ac_dir)]))
-AS_VAR_POPDEF([ac_enable])])dnl
-m4_popdef([ac_dir])dnl
-m4_popdef([ac_name])])
+AS_VAR_PUSHDEF([ac_enable],m4_default([$2],[enable_]$1))dnl
+wine_fn_config_makefile [$1] ac_enable[]dnl
+AS_VAR_POPDEF([ac_enable])])
 
 dnl **** Create a dll makefile from config.status ****
 dnl
diff --git a/configure b/configure
index 346ec70e950..6363a24af1d 100755
--- a/configure
+++ b/configure
@@ -13782,8 +13782,11 @@ esac
 
 ac_config_commands="$ac_config_commands include/stamp-h"
 
+ac_config_files="$ac_config_files Makefile"
 
-ALL_MAKEFILE_DEPENDS="# Makefile dependencies"
+
+ALL_MAKEFILE_DEPENDS="# Makefile dependencies
+Makefile: Makefile.in Make.rules config.status"
 
 ALL_WINETEST_DEPENDS="# Test binaries"
 
@@ -13830,12 +13833,21 @@ wine_fn_append_rule ()
 wine_fn_config_makefile ()
 {
     ac_dir=$1
-    ac_deps=$2
+    ac_enable=$2
     wine_fn_append_file ALL_DIRS $ac_dir
     wine_fn_append_rule ALL_MAKEFILE_DEPENDS \
 "$ac_dir/__clean__ $ac_dir/__install__ $ac_dir/__install-dev__ $ac_dir/__install-lib__ $ac_dir/__uninstall__ $ac_dir: $ac_dir/Makefile
-$ac_dir/Makefile $ac_dir/__depend__: $ac_dir/Makefile.in config.status $ac_deps
+$ac_dir/Makefile $ac_dir/__depend__: $ac_dir/Makefile.in config.status Make.rules \$(MAKEDEP)
 	@./config.status --file $ac_dir/Makefile && cd $ac_dir && \$(MAKE) depend"
+    eval as_val=\$$ac_enable
+   if test "x$as_val" = x""no; then :
+
+else
+  case $ac_dir in
+                 */*) ;;
+                 *) wine_fn_append_file ALL_TOP_DIRS $ac_dir ;;
+               esac
+fi
 }
 
 wine_fn_config_lib ()
@@ -14029,9 +14041,6 @@ MAKE_PROG_RULES=programs/Makeprog.rules
 ac_config_files="$ac_config_files programs/Makeprog.rules"
 
 
-wine_fn_append_rule ALL_MAKEFILE_DEPENDS "Makefile: Makefile.in Make.rules config.status"
-ac_config_files="$ac_config_files Makefile"
-
 wine_fn_config_dll acledit enable_acledit
 wine_fn_config_dll aclui enable_aclui aclui
 wine_fn_config_dll activeds enable_activeds activeds
@@ -14505,30 +14514,14 @@ wine_fn_config_test dlls/xinput1_3/tests xinput1_3_test
 wine_fn_config_dll xinput9_1_0 enable_xinput9_1_0
 wine_fn_config_dll xmllite enable_xmllite
 wine_fn_config_test dlls/xmllite/tests xmllite_test
-wine_fn_config_makefile documentation "Make.rules \$(MAKEDEP)"
-test "x$enable_documentation" != xno && wine_fn_append_file ALL_TOP_DIRS "documentation"
-
-wine_fn_config_makefile fonts "Make.rules \$(MAKEDEP)"
-test "x$enable_fonts" != xno && wine_fn_append_file ALL_TOP_DIRS "fonts"
-
-wine_fn_config_makefile include "Make.rules \$(MAKEDEP)"
-test "x$enable_include" != xno && wine_fn_append_file ALL_TOP_DIRS "include"
-
-wine_fn_config_makefile libs/port "Make.rules \$(MAKEDEP)"
-
-
-wine_fn_config_makefile libs/wine "Make.rules \$(MAKEDEP)"
-
-
-wine_fn_config_makefile libs/wpp "Make.rules \$(MAKEDEP)"
-
-
-wine_fn_config_makefile loader "Make.rules \$(MAKEDEP)"
-test "x$enable_loader" != xno && wine_fn_append_file ALL_TOP_DIRS "loader"
-
-wine_fn_config_makefile programs "Make.rules \$(MAKEDEP)"
-test "x$enable_programs" != xno && wine_fn_append_file ALL_TOP_DIRS "programs"
-
+wine_fn_config_makefile documentation enable_documentation
+wine_fn_config_makefile fonts enable_fonts
+wine_fn_config_makefile include enable_include
+wine_fn_config_makefile libs/port enable_libs_port
+wine_fn_config_makefile libs/wine enable_libs_wine
+wine_fn_config_makefile libs/wpp enable_libs_wpp
+wine_fn_config_makefile loader enable_loader
+wine_fn_config_makefile programs enable_programs
 wine_fn_config_program attrib enable_attrib install
 wine_fn_config_program cacls enable_cacls install
 wine_fn_config_program clock enable_clock install
@@ -14586,9 +14579,7 @@ wine_fn_config_program winver enable_winver install
 wine_fn_config_program wordpad enable_wordpad install
 wine_fn_config_program write enable_write install
 wine_fn_config_program xcopy enable_xcopy install
-wine_fn_config_makefile server "Make.rules \$(MAKEDEP)"
-test "x$enable_server" != xno && wine_fn_append_file ALL_TOP_DIRS "server"
-
+wine_fn_config_makefile server enable_server
 wine_fn_config_tool tools
 wine_fn_config_tool tools/widl
 wine_fn_config_tool tools/winebuild
@@ -15293,6 +15284,7 @@ do
   case $ac_config_target in
     "include/config.h") CONFIG_HEADERS="$CONFIG_HEADERS include/config.h" ;;
     "include/stamp-h") CONFIG_COMMANDS="$CONFIG_COMMANDS include/stamp-h" ;;
+    "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
     "dlls/wineps.drv/generic.ppd") CONFIG_LINKS="$CONFIG_LINKS dlls/wineps.drv/generic.ppd:dlls/wineps.drv/generic.ppd" ;;
     "fonts/marlett.ttf") CONFIG_LINKS="$CONFIG_LINKS fonts/marlett.ttf:fonts/marlett.ttf" ;;
     "fonts/symbol.ttf") CONFIG_LINKS="$CONFIG_LINKS fonts/symbol.ttf:fonts/symbol.ttf" ;;
@@ -15310,16 +15302,6 @@ do
     "dlls/Makedll.rules") CONFIG_FILES="$CONFIG_FILES dlls/Makedll.rules" ;;
     "dlls/Makeimplib.rules") CONFIG_FILES="$CONFIG_FILES dlls/Makeimplib.rules" ;;
     "programs/Makeprog.rules") CONFIG_FILES="$CONFIG_FILES programs/Makeprog.rules" ;;
-    "Makefile") CONFIG_FILES="$CONFIG_FILES Makefile" ;;
-    "documentation/Makefile") CONFIG_FILES="$CONFIG_FILES documentation/Makefile" ;;
-    "fonts/Makefile") CONFIG_FILES="$CONFIG_FILES fonts/Makefile" ;;
-    "include/Makefile") CONFIG_FILES="$CONFIG_FILES include/Makefile" ;;
-    "libs/port/Makefile") CONFIG_FILES="$CONFIG_FILES libs/port/Makefile" ;;
-    "libs/wine/Makefile") CONFIG_FILES="$CONFIG_FILES libs/wine/Makefile" ;;
-    "libs/wpp/Makefile") CONFIG_FILES="$CONFIG_FILES libs/wpp/Makefile" ;;
-    "loader/Makefile") CONFIG_FILES="$CONFIG_FILES loader/Makefile" ;;
-    "programs/Makefile") CONFIG_FILES="$CONFIG_FILES programs/Makefile" ;;
-    "server/Makefile") CONFIG_FILES="$CONFIG_FILES server/Makefile" ;;
 
   *) as_fn_error "invalid argument: \`$ac_config_target'" "$LINENO" 5;;
   esac
diff --git a/configure.ac b/configure.ac
index a22b9845194..5655b512ca1 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2121,6 +2121,7 @@ dnl **** Generate output files ****
 AH_TOP([#define __WINE_CONFIG_H])
 
 AC_CONFIG_COMMANDS([include/stamp-h], [echo timestamp > include/stamp-h])
+AC_CONFIG_FILES([Makefile])
 
 WINE_CONFIG_SYMLINK(dlls/wineps.drv/generic.ppd)
 WINE_CONFIG_SYMLINK(fonts/marlett.ttf)
@@ -2142,7 +2143,6 @@ WINE_CONFIG_MAKERULES([dlls/Makedll.rules],[MAKE_DLL_RULES],[Make.rules])
 WINE_CONFIG_MAKERULES([dlls/Makeimplib.rules],[MAKE_IMPLIB_RULES],[Make.rules])
 WINE_CONFIG_MAKERULES([programs/Makeprog.rules],[MAKE_PROG_RULES],[Make.rules])
 
-WINE_CONFIG_MAKEFILE([Makefile],[Make.rules])
 WINE_CONFIG_DLL(acledit)
 WINE_CONFIG_DLL(aclui,,[aclui])
 WINE_CONFIG_DLL(activeds,,[activeds])
@@ -2616,14 +2616,14 @@ WINE_CONFIG_TEST(dlls/xinput1_3/tests)
 WINE_CONFIG_DLL(xinput9_1_0)
 WINE_CONFIG_DLL(xmllite)
 WINE_CONFIG_TEST(dlls/xmllite/tests)
-WINE_CONFIG_MAKEFILE([documentation/Makefile],[Make.rules],[ALL_TOP_DIRS])
-WINE_CONFIG_MAKEFILE([fonts/Makefile],[Make.rules],[ALL_TOP_DIRS])
-WINE_CONFIG_MAKEFILE([include/Makefile],[Make.rules],[ALL_TOP_DIRS])
-WINE_CONFIG_MAKEFILE([libs/port/Makefile],[Make.rules])
-WINE_CONFIG_MAKEFILE([libs/wine/Makefile],[Make.rules])
-WINE_CONFIG_MAKEFILE([libs/wpp/Makefile],[Make.rules])
-WINE_CONFIG_MAKEFILE([loader/Makefile],[Make.rules],[ALL_TOP_DIRS])
-WINE_CONFIG_MAKEFILE([programs/Makefile],[Make.rules],[ALL_TOP_DIRS])
+WINE_CONFIG_MAKEFILE([documentation])
+WINE_CONFIG_MAKEFILE([fonts])
+WINE_CONFIG_MAKEFILE([include])
+WINE_CONFIG_MAKEFILE([libs/port])
+WINE_CONFIG_MAKEFILE([libs/wine])
+WINE_CONFIG_MAKEFILE([libs/wpp])
+WINE_CONFIG_MAKEFILE([loader])
+WINE_CONFIG_MAKEFILE([programs])
 WINE_CONFIG_PROGRAM(attrib,install)
 WINE_CONFIG_PROGRAM(cacls,install)
 WINE_CONFIG_PROGRAM(clock,install)
@@ -2681,7 +2681,7 @@ WINE_CONFIG_PROGRAM(winver,install)
 WINE_CONFIG_PROGRAM(wordpad,install)
 WINE_CONFIG_PROGRAM(write,install)
 WINE_CONFIG_PROGRAM(xcopy,install)
-WINE_CONFIG_MAKEFILE([server/Makefile],[Make.rules],[ALL_TOP_DIRS])
+WINE_CONFIG_MAKEFILE([server])
 WINE_CONFIG_TOOL(tools)
 WINE_CONFIG_TOOL(tools/widl)
 WINE_CONFIG_TOOL(tools/winebuild)
diff --git a/tools/make_makefiles b/tools/make_makefiles
index 33fcbc0031c..83d7836dc90 100755
--- a/tools/make_makefiles
+++ b/tools/make_makefiles
@@ -395,13 +395,10 @@ sub update_makefiles(@)
             (my $name = $file) =~ s/^(.*)\/Makefile/$1/;
             push @lines, "WINE_CONFIG_TOOL($name)\n";
         }
-        elsif ($file =~ /^[^\/]*\/Makefile$/)
+        elsif ($file =~ /\/Makefile$/)
         {
-            push @lines, "WINE_CONFIG_MAKEFILE([$file],[$rules],[ALL_TOP_DIRS])\n";
-        }
-        else
-        {
-            push @lines, "WINE_CONFIG_MAKEFILE([$file],[$rules])\n";
+            (my $name = $file) =~ s/^(.*)\/Makefile/$1/;
+            push @lines, "WINE_CONFIG_MAKEFILE([$name])\n";
         }
     }