diff --git a/.gitignore b/.gitignore
index d0cf776..bb19dad 100644
--- a/.gitignore
+++ b/.gitignore
@@ -235,7 +235,6 @@
 programs/rpcss/irot_s.c
 programs/services/svcctl.h
 programs/services/svcctl_s.c
-programs/wineapploader
 programs/winedbg/dbg.tab.c
 programs/winedbg/dbg.tab.h
 programs/winedbg/debug.yy.c
@@ -260,6 +259,7 @@
 tools/widl/widl
 tools/widl/widl.man
 tools/wine.inf
+tools/wineapploader
 tools/winebuild/winebuild
 tools/winebuild/winebuild.man
 tools/winedump/winedump
diff --git a/Makefile.in b/Makefile.in
index 62ac1f6..67507a1 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -24,7 +24,7 @@
 VPATH     = @srcdir@
 
 # Sub-directories that don't have a makefile
-EXTRASUBDIRS = dlls libs
+EXTRASUBDIRS = dlls libs programs
 
 # Destination directories for make install
 INSTALLDIRS = $(DESTDIR)$(bindir)
diff --git a/aclocal.m4 b/aclocal.m4
index 1735fd0..3a7765f 100644
--- a/aclocal.m4
+++ b/aclocal.m4
@@ -296,11 +296,11 @@
 	@cd programs/$ac_dir && \$(MAKE) install
 uninstall:: programs/$ac_dir/Makefile
 	@cd programs/$ac_dir && \$(MAKE) uninstall"
-    if test "$ac_install" = installbin -a -n "$DLLEXT" -a -z "$WOW64_DISABLE"
+    if test "$ac_install" = installbin -a -n "$DLLEXT" -a "x$enable_tools" != xno
     then
         wine_fn_append_rule ALL_MAKEFILE_DEPENDS \
-"install install-lib:: programs \$(DESTDIR)\$(bindir)
-	\$(INSTALL_SCRIPT) programs/wineapploader \$(DESTDIR)\$(bindir)/$ac_dir
+"install install-lib:: tools \$(DESTDIR)\$(bindir)
+	\$(INSTALL_SCRIPT) tools/wineapploader \$(DESTDIR)\$(bindir)/$ac_dir
 uninstall::
 	\$(RM) \$(DESTDIR)\$(bindir)/$ac_dir"
     fi])
diff --git a/configure b/configure
index 74a51a8..3186e81 100755
--- a/configure
+++ b/configure
@@ -14009,11 +14009,11 @@
 	@cd programs/$ac_dir && \$(MAKE) install
 uninstall:: programs/$ac_dir/Makefile
 	@cd programs/$ac_dir && \$(MAKE) uninstall"
-    if test "$ac_install" = installbin -a -n "$DLLEXT" -a -z "$WOW64_DISABLE"
+    if test "$ac_install" = installbin -a -n "$DLLEXT" -a "x$enable_tools" != xno
     then
         wine_fn_append_rule ALL_MAKEFILE_DEPENDS \
-"install install-lib:: programs \$(DESTDIR)\$(bindir)
-	\$(INSTALL_SCRIPT) programs/wineapploader \$(DESTDIR)\$(bindir)/$ac_dir
+"install install-lib:: tools \$(DESTDIR)\$(bindir)
+	\$(INSTALL_SCRIPT) tools/wineapploader \$(DESTDIR)\$(bindir)/$ac_dir
 uninstall::
 	\$(RM) \$(DESTDIR)\$(bindir)/$ac_dir"
     fi
@@ -14633,7 +14633,6 @@
 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
diff --git a/configure.ac b/configure.ac
index 68d6f45..fc05f10 100644
--- a/configure.ac
+++ b/configure.ac
@@ -2634,7 +2634,6 @@
 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)
diff --git a/programs/Makefile.in b/programs/Makefile.in
deleted file mode 100644
index ebb7547..0000000
--- a/programs/Makefile.in
+++ /dev/null
@@ -1,13 +0,0 @@
-TOPSRCDIR = @top_srcdir@
-TOPOBJDIR = ..
-SRCDIR    = @srcdir@
-VPATH     = @srcdir@
-
-PROGRAMS = wineapploader
-
-@MAKE_RULES@
-
-all: $(PROGRAMS)
-
-wineapploader: wineapploader.in
-	sed -e 's,@bindir\@,$(bindir),g' $(SRCDIR)/wineapploader.in >$@ || ($(RM) $@ && false)
diff --git a/tools/Makefile.in b/tools/Makefile.in
index 2dd6f8a..5e005e0 100644
--- a/tools/Makefile.in
+++ b/tools/Makefile.in
@@ -15,6 +15,7 @@
 	relpath$(EXEEXT) \
 	sfnt2fnt$(EXEEXT) \
 	wine.inf \
+	wineapploader \
 	wineprefixcreate
 
 MANPAGES = \
@@ -64,6 +65,9 @@
 wine.inf: wine.inf.in
 	LC_ALL=C sed -e 's,@PACKAGE_STRING\@,@PACKAGE_STRING@,g' $(SRCDIR)/wine.inf.in >$@ || ($(RM) $@ && false)
 
+wineapploader: wineapploader.in
+	sed -e 's,@bindir\@,$(bindir),g' $(SRCDIR)/wineapploader.in >$@ || ($(RM) $@ && false)
+
 wineprefixcreate: wineprefixcreate.in relpath$(EXEEXT)
 	sed -e "s,@bintodlldir\@,`$(RELPATH) $(bindir) $(dlldir)`,g" -e "s,@bintodatadir\@,`$(RELPATH) $(bindir) $(datadir)/wine`,g" $(SRCDIR)/wineprefixcreate.in >$@ || ($(RM) $@ && false)
 	chmod +x wineprefixcreate
diff --git a/programs/wineapploader.in b/tools/wineapploader.in
similarity index 100%
rename from programs/wineapploader.in
rename to tools/wineapploader.in