diff --git a/Make.rules.in b/Make.rules.in
index 27e56672f2..59481807a6 100644
--- a/Make.rules.in
+++ b/Make.rules.in
@@ -19,7 +19,6 @@ RCFLAGS      = --nostdinc $(PORCFLAGS) $(TARGETFLAGS) $(DEFS) $(EXTRARCFLAGS)
 IDL_GEN_C_SRCS  = $(IDL_C_SRCS:.idl=_c.c) $(IDL_I_SRCS:.idl=_i.c) \
                   $(IDL_P_SRCS:.idl=_p.c) $(IDL_S_SRCS:.idl=_s.c)
 
-CLEAN_FILES   = *.o *.a *.so *.res *.fake *.ok *.tab.[ch] *.yy.c
 CLEAN_TARGETS = $(MODULE) $(IMPORTLIB:%=lib%.@IMPLIBEXT@) \
                 $(TESTMODULE) $(TESTMODULE_STRIPPED) $(CROSSTESTMODULE)
 
diff --git a/Make.vars.in b/Make.vars.in
index ac74f1f670..7b6e265fb4 100644
--- a/Make.vars.in
+++ b/Make.vars.in
@@ -76,6 +76,7 @@ INSTALL         = @INSTALL@ $(INSTALL_FLAGS)
 INSTALL_PROGRAM = @INSTALL_PROGRAM@ $(INSTALL_PROGRAM_FLAGS)
 INSTALL_SCRIPT  = @INSTALL_SCRIPT@ $(INSTALL_SCRIPT_FLAGS)
 INSTALL_DATA    = @INSTALL_DATA@ $(INSTALL_DATA_FLAGS)
+CLEAN_FILES     = *.o *.a *.so *.res *.fake *.ok *.tab.[ch] *.yy.c
 prog_manext     = 1
 api_manext      = 3w
 conf_manext     = 5
diff --git a/Makefile.in b/Makefile.in
index c2bb1ed4ca..c7889d00e0 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -28,8 +28,6 @@ INSTALLDIRS = \
 all: wine
 	@echo "Wine build complete."
 
-@MAKE_RULES@
-
 # Rules for re-running configure
 
 config.status: $(srcdir)/configure
@@ -41,15 +39,19 @@ include/stamp-h: $(srcdir)/include/config.h.in config.status
 
 # Rules for cleaning
 
-.PHONY: __clean__
+.PHONY: clean distclean __clean__
+
 clean:: __clean__
 distclean:: clean
 	$(RM) config.* configure.lineno TAGS tags include/config.h include/stamp-h Makefile Make.tmp
 	$(RM) -r autom4te.cache
 
-# Rules for uninstalling
+# Rules for installing
 
-.PHONY: __uninstall__
+$(INSTALLDIRS):
+	$(MKDIR_P) -m 755 $@
+
+.PHONY: install install-lib install-dev uninstall __uninstall__
 uninstall:: __uninstall__
 	-rmdir $(DESTDIR)$(datadir)/wine $(DESTDIR)$(fakedlldir) $(DESTDIR)$(dlldir)
 
@@ -58,7 +60,7 @@ uninstall:: __uninstall__
 # dependencies needed to build any dll or program
 __tooldeps__: libs/port libs/wine libs/wpp
 __builddeps__: __tooldeps__ include
-.PHONY: check test testclean crosstest __tooldeps__ __builddeps__
+.PHONY: depend check test testclean crosstest __tooldeps__ __builddeps__
 
 loader server: libs/port libs/wine tools
 fonts: tools
diff --git a/configure b/configure
index 8fde22689e..e60430136a 100755
--- a/configure
+++ b/configure
@@ -16681,7 +16681,7 @@ wine_fn_append_rule "
 .INIT: Makefile
 .MAKEFILEDEPS:
 all: Makefile
-Makefile: $srcdir/Makefile.in $srcdir/Make.vars.in Make.rules config.status
+Makefile: $srcdir/Makefile.in $srcdir/Make.vars.in config.status
 	@./config.status Make.tmp Makefile"
 
 if test "x$enable_fonts" != xno; then
@@ -17525,7 +17525,7 @@ then
     ac_config_commands="$ac_config_commands tools"
 
     wine_fn_append_rule "tools/makedep$ac_exeext: $srcdir/tools/makedep.c include/config.h
-	\$(CC) -Iinclude -I$srcdir/include \$(ALLCFLAGS) -o \$@ $srcdir/tools/makedep.c \$(LDFLAGS)
+	\$(CC) -Iinclude -I$srcdir/include -D__WINESRC__ \$(EXTRACFLAGS) \$(CPPFLAGS) \$(CFLAGS) -o \$@ $srcdir/tools/makedep.c \$(LDFLAGS)
 clean:: __clean__
 	\$(RM) tools/makedep$ac_exeext"
 else
diff --git a/configure.ac b/configure.ac
index 34b7a52e2f..fc6cdde3de 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2664,7 +2664,7 @@ WINE_APPEND_RULE([
 .INIT: Makefile
 .MAKEFILEDEPS:
 all: Makefile
-Makefile: $srcdir/Makefile.in $srcdir/Make.vars.in Make.rules config.status
+Makefile: $srcdir/Makefile.in $srcdir/Make.vars.in config.status
 	@./config.status Make.tmp Makefile])
 
 WINE_CONFIG_SYMLINK(fonts,fonts,[marlett.ttf,symbol.ttf,tahoma.ttf,tahomabd.ttf],enable_fonts)
@@ -3502,7 +3502,7 @@ then
     AC_CONFIG_COMMANDS([tools],[AS_MKDIR_P(tools)])
     WINE_APPEND_RULE(
 [tools/makedep$ac_exeext: $srcdir/tools/makedep.c include/config.h
-	\$(CC) -Iinclude -I$srcdir/include \$(ALLCFLAGS) -o \$@ $srcdir/tools/makedep.c \$(LDFLAGS)
+	\$(CC) -Iinclude -I$srcdir/include -D__WINESRC__ \$(EXTRACFLAGS) \$(CPPFLAGS) \$(CFLAGS) -o \$@ $srcdir/tools/makedep.c \$(LDFLAGS)
 clean:: __clean__
 	\$(RM) tools/makedep$ac_exeext])
 else
diff --git a/tools/make_makefiles b/tools/make_makefiles
index 13106e7f96..34fef855df 100755
--- a/tools/make_makefiles
+++ b/tools/make_makefiles
@@ -543,6 +543,7 @@ sub update_makefiles(@)
     foreach my $file (sort @_)
     {
         my %make = %{$makefiles{$file}};
+        next unless defined $make{"=rules"};
         my $rules = $make{"=rules"};
         my $args = "";
         my $is_win16 = $make{"MODULE"} && ($make{"MODULE"} =~ /16$/ || $modules16{$make{"MODULE"}});