diff --git a/Makefile.am b/Makefile.am
index 28a7ef7..dbbf47b 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -50,23 +50,16 @@
 	config-version.h
 endif
 
-SUBDIRS = build distro include src sample doc tests
+SUBDIRS = include src
 
 dist_doc_DATA = \
-	README \
+	README.openvpn \
 	README.IPv6 \
-	README.mbedtls \
-	Changes.rst \
-	COPYRIGHT.GPL \
-	COPYING
+	LICENSE
 
 dist_noinst_DATA = \
-	.gitignore \
-	.gitattributes \
-	PORTS \
-	README.IPv6 TODO.IPv6 \
-	README.mbedtls \
-	openvpn.sln
+	README.openvpn \
+	README.IPv6
 
 dist_noinst_HEADERS = \
 	config-msvc.h \
diff --git a/configure.ac b/configure.ac
index 2f5f6bc..25df1b8 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1450,33 +1450,12 @@
 AC_CONFIG_FILES([
 	version.sh
 	Makefile
-	build/Makefile
-	build/msvc/Makefile
-	build/msvc/msvc-generate/Makefile
-	distro/Makefile
-	distro/systemd/Makefile
-	doc/Makefile
-	doc/doxygen/Makefile
-	doc/doxygen/openvpn.doxyfile
 	include/Makefile
-	sample/sample-plugins/Makefile
 	src/Makefile
 	src/compat/Makefile
 	src/openvpn/Makefile
-	src/openvpnmsica/Makefile
-	src/openvpnserv/Makefile
 	src/plugins/Makefile
-	src/plugins/auth-pam/Makefile
 	src/plugins/down-root/Makefile
 	src/tapctl/Makefile
-	tests/Makefile
-        tests/unit_tests/Makefile
-        tests/unit_tests/example_test/Makefile
-        tests/unit_tests/openvpn/Makefile
-        tests/unit_tests/plugins/Makefile
-        tests/unit_tests/plugins/auth-pam/Makefile
-	tests/unit_tests/engine-key/Makefile
-	sample/Makefile
 ])
-AC_CONFIG_FILES([tests/t_client.sh], [chmod +x tests/t_client.sh])
 AC_OUTPUT
diff --git a/patches/cleanup_makefiles.patch b/patches/cleanup_makefiles.patch
index 8c4942c..cb5da31 100644
--- a/patches/cleanup_makefiles.patch
+++ b/patches/cleanup_makefiles.patch
@@ -1,8 +1,6 @@
-Index: openvpn/Makefile.am
-===================================================================
---- openvpn.orig/Makefile.am
-+++ openvpn/Makefile.am
-@@ -50,26 +50,16 @@ BUILT_SOURCES = \
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -50,23 +50,16 @@ BUILT_SOURCES = \
  	config-version.h
  endif
  
@@ -25,53 +23,15 @@
 -	PORTS \
 -	README.IPv6 TODO.IPv6 \
 -	README.mbedtls \
--	openvpn.sln \
--	msvc-env.bat \
--	msvc-dev.bat \
--	msvc-build.bat
+-	openvpn.sln
 +	README.openvpn \
 +	README.IPv6
  
  dist_noinst_HEADERS = \
  	config-msvc.h \
-Index: openvpn/src/Makefile.am
-===================================================================
---- openvpn.orig/src/Makefile.am
-+++ openvpn/src/Makefile.am
-@@ -12,4 +12,4 @@
- MAINTAINERCLEANFILES = \
- 	$(srcdir)/Makefile.in
- 
--SUBDIRS = compat openvpn openvpnmsica openvpnserv plugins tapctl
-+SUBDIRS = compat openvpn plugins
-Index: openvpn/src/openvpn/Makefile.am
-===================================================================
---- openvpn.orig/src/openvpn/Makefile.am
-+++ openvpn/src/openvpn/Makefile.am
-@@ -9,7 +9,7 @@
- #  Copyright (C) 2006-2012 Alon Bar-Lev <alon.barlev@gmail.com>
- #
- 
--include $(top_srcdir)/build/ltrc.inc
-+include $(top_srcdir)/ltrc.inc
- 
- MAINTAINERCLEANFILES = \
- 	$(srcdir)/Makefile.in
-Index: openvpn/src/plugins/Makefile.am
-===================================================================
---- openvpn.orig/src/plugins/Makefile.am
-+++ openvpn/src/plugins/Makefile.am
-@@ -12,4 +12,4 @@
- MAINTAINERCLEANFILES = \
- 	$(srcdir)/Makefile.in
- 
--SUBDIRS = auth-pam down-root
-+SUBDIRS = down-root
-Index: openvpn/configure.ac
-===================================================================
---- openvpn.orig/configure.ac
-+++ openvpn/configure.ac
-@@ -1424,33 +1424,12 @@ AC_SUBST([TEST_CFLAGS])
+--- a/configure.ac
++++ b/configure.ac
+@@ -1450,33 +1450,12 @@ AC_SUBST([TEST_CFLAGS])
  AC_CONFIG_FILES([
  	version.sh
  	Makefile
@@ -105,10 +65,27 @@
  ])
 -AC_CONFIG_FILES([tests/t_client.sh], [chmod +x tests/t_client.sh])
  AC_OUTPUT
-Index: openvpn/src/openvpnmsica/Makefile.am
-===================================================================
---- openvpn.orig/src/openvpnmsica/Makefile.am
-+++ openvpn/src/openvpnmsica/Makefile.am
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -12,4 +12,4 @@
+ MAINTAINERCLEANFILES = \
+ 	$(srcdir)/Makefile.in
+ 
+-SUBDIRS = compat openvpn openvpnmsica openvpnserv plugins tapctl
++SUBDIRS = compat openvpn plugins
+--- a/src/openvpn/Makefile.am
++++ b/src/openvpn/Makefile.am
+@@ -9,7 +9,7 @@
+ #  Copyright (C) 2006-2012 Alon Bar-Lev <alon.barlev@gmail.com>
+ #
+ 
+-include $(top_srcdir)/build/ltrc.inc
++include $(top_srcdir)/ltrc.inc
+ 
+ MAINTAINERCLEANFILES = \
+ 	$(srcdir)/Makefile.in
+--- a/src/openvpnmsica/Makefile.am
++++ b/src/openvpnmsica/Makefile.am
 @@ -18,7 +18,7 @@
  #  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
@@ -118,10 +95,16 @@
  
  MAINTAINERCLEANFILES = $(srcdir)/Makefile.in
  
-Index: openvpn/src/tapctl/Makefile.am
-===================================================================
---- openvpn.orig/src/tapctl/Makefile.am
-+++ openvpn/src/tapctl/Makefile.am
+--- a/src/plugins/Makefile.am
++++ b/src/plugins/Makefile.am
+@@ -12,4 +12,4 @@
+ MAINTAINERCLEANFILES = \
+ 	$(srcdir)/Makefile.in
+ 
+-SUBDIRS = auth-pam down-root
++SUBDIRS = down-root
+--- a/src/tapctl/Makefile.am
++++ b/src/tapctl/Makefile.am
 @@ -18,7 +18,7 @@
  #  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
  #
diff --git a/patches/series b/patches/series
index f7b5bd2..c79e662 100644
--- a/patches/series
+++ b/patches/series
@@ -1,3 +1,4 @@
 remove_autoconf_vars.patch
 add_missing_licenses.patch
 fix_long_password.patch
+cleanup_makefiles.patch
diff --git a/src/Makefile.am b/src/Makefile.am
index 40bcda2..ad66d05 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -12,4 +12,4 @@
 MAINTAINERCLEANFILES = \
 	$(srcdir)/Makefile.in
 
-SUBDIRS = compat openvpn openvpnmsica openvpnserv plugins tapctl
+SUBDIRS = compat openvpn plugins
diff --git a/src/openvpn/Makefile.am b/src/openvpn/Makefile.am
index 2c52200..1c62910 100644
--- a/src/openvpn/Makefile.am
+++ b/src/openvpn/Makefile.am
@@ -9,7 +9,7 @@
 #  Copyright (C) 2006-2012 Alon Bar-Lev <alon.barlev@gmail.com>
 #
 
-include $(top_srcdir)/build/ltrc.inc
+include $(top_srcdir)/ltrc.inc
 
 MAINTAINERCLEANFILES = \
 	$(srcdir)/Makefile.in
diff --git a/src/openvpnmsica/Makefile.am b/src/openvpnmsica/Makefile.am
index a1a04af..8ba9e12 100644
--- a/src/openvpnmsica/Makefile.am
+++ b/src/openvpnmsica/Makefile.am
@@ -18,7 +18,7 @@
 #  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 #
 
-include $(top_srcdir)/build/ltrc.inc
+include $(top_srcdir)/ltrc.inc
 
 MAINTAINERCLEANFILES = $(srcdir)/Makefile.in
 
diff --git a/src/plugins/Makefile.am b/src/plugins/Makefile.am
index 4c72bf0..07211a9 100644
--- a/src/plugins/Makefile.am
+++ b/src/plugins/Makefile.am
@@ -12,4 +12,4 @@
 MAINTAINERCLEANFILES = \
 	$(srcdir)/Makefile.in
 
-SUBDIRS = auth-pam down-root
+SUBDIRS = down-root
diff --git a/src/tapctl/Makefile.am b/src/tapctl/Makefile.am
index 305181b..8d0103a 100644
--- a/src/tapctl/Makefile.am
+++ b/src/tapctl/Makefile.am
@@ -18,7 +18,7 @@
 #  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 #
 
-include $(top_srcdir)/build/ltrc.inc
+include $(top_srcdir)/ltrc.inc
 
 MAINTAINERCLEANFILES = $(srcdir)/Makefile.in