diff --git a/Makefile.am b/Makefile.am
index 93c29f0ee29524032a267510611b1811847feec2..060dc96c4ecab84a8730fa4db2234947b45464e3 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -1,3 +1,4 @@
-SUBDIRS = include libmpeg2 libvo doc src vc++ test
+SUBDIRS = libmpeg2 libvo src test
+DIST_SUBDIRS = include doc vc++ $(SUBDIRS)
 
 EXTRA_DIST = bootstrap CodingStyle
diff --git a/bootstrap b/bootstrap
index aeb2580cde0b0e3b4e087e93ecb8ff12507c27f2..53ba8abc0533578b22a03e0d697492fbacd7616c 100755
--- a/bootstrap
+++ b/bootstrap
@@ -1,11 +1,14 @@
 #! /bin/sh
+# $Id$
 
-# bootstrap: the ultimate bootstrap/autogen.sh script for autotools projects
-# Copyright (c) 2002, 2003, 2004, 2005, 2006 Sam Hocevar <sam@zoy.org>
+# bootstrap: generic bootstrap/autogen.sh script for autotools projects
 #
-#    This program is free software; you can redistribute it and/or
-#    modify it under the terms of the Do What The Fuck You Want To
-#    Public License, Version 2, as published by Sam Hocevar. See
+# Copyright (c) 2002-2007 Sam Hocevar <sam@zoy.org>
+#
+#    This program is free software. It comes without any warranty, to
+#    the extent permitted by applicable law. You can redistribute it
+#    and/or modify it under the terms of the Do What The Fuck You Want
+#    To Public License, Version 2, as published by Sam Hocevar. See
 #    http://sam.zoy.org/wtfpl/COPYING for more details.
 #
 # The latest version of this script can be found at the following place:
@@ -25,19 +28,33 @@ else
 fi
 
 # Check for needed features
-auxdir="`sed -ne 's/^[ \t]*A._CONFIG_AUX_DIR *( *\([^ )]*\).*/\1/p' $conffile`"
+auxdir="`sed -ne 's/^[ \t]*A._CONFIG_AUX_DIR *([[ ]*\([^] )]*\).*/\1/p' $conffile`"
 libtool="`grep -q '^[ \t]*A._PROG_LIBTOOL' $conffile && echo yes || echo no`"
+pkgconfig="`grep -q '^[ \t]*PKG_PROG_PKG_CONFIG' $conffile && echo yes || echo no`"
 header="`grep -q '^[ \t]*A._CONFIG_HEADER' $conffile && echo yes || echo no`"
+aclocalflags="`sed -ne 's/^[ \t]*ACLOCAL_AMFLAGS[ \t]*=//p' Makefile.am`"
 
 # Check for automake
 amvers="no"
-for v in "-1.10" "110" "-1.9" "19" "-1.8" "18" "-1.7" "17" "-1.6" "16" "-1.5" "15" ""; do
-  if automake${v} --version >/dev/null 2>&1; then
-    amvers="${v}"
+for v in 10 9 8 7 6 5; do
+  if automake-1.${v} --version >/dev/null 2>&1; then
+    amvers="-1.${v}"
+    break
+  elif automake1.${v} --version >/dev/null 2>&1; then
+    amvers="1.${v}"
     break
   fi
 done
 
+if test "${amvers}" = "no" && automake --version > /dev/null 2>&1; then
+  amvers="`automake --version | sed -e '1s/[^0-9]*//' -e q`"
+  if expr "$amvers" "<" "1.5" > /dev/null 2>&1; then
+    amvers="no"
+  else
+    amvers=""
+  fi
+fi
+
 if test "$amvers" = "no"; then
   echo "$0: you need automake version 1.5 or later"
   exit 1
@@ -77,10 +94,23 @@ if test "$libtool" = "yes"; then
   fi
 fi
 
+# Check for pkg-config
+if test "$pkgconfig" = "yes"; then
+  if ! pkg-config --version >/dev/null 2>&1; then
+    echo "$0: you need pkg-config"
+    exit 1
+  fi
+fi
+
 # Remove old cruft
 for x in aclocal.m4 configure config.guess config.log config.sub config.cache config.h.in config.h compile libtool.m4 ltoptions.m4 ltsugar.m4 ltversion.m4 ltmain.sh libtool ltconfig missing mkinstalldirs depcomp install-sh; do rm -f $x autotools/$x; if test -n "$auxdir"; then rm -f "$auxdir/$x"; fi; done
 rm -Rf autom4te.cache
-if test -n "$auxdir" -a ! -d "$auxdir"; then mkdir "$auxdir"; fi
+if test -n "$auxdir"; then
+  if test ! -d "$auxdir"; then
+    mkdir "$auxdir"
+  fi
+  aclocalflags="${aclocalflags} -I $auxdir -I ."
+fi
 
 # Explain what we are doing from now
 set -x
@@ -88,17 +118,13 @@ set -x
 # Bootstrap package
 if test "$libtool" = "yes"; then
   ${libtoolize} --copy --force
-  if test -n "$auxdir" -a -f "ltmain.sh"; then
+  if test -n "$auxdir" -a ! "$auxdir" = "." -a -f "ltmain.sh"; then
     echo "$0: working around a minor libtool issue"
     mv ltmain.sh "$auxdir/"
   fi
 fi
 
-if test -n "$auxdir"; then
-  aclocal${amvers} -I autotools
-else
-  aclocal${amvers}
-fi
+aclocal${amvers} ${aclocalflags}
 autoconf${acvers}
 if test "$header" = "yes"; then
   autoheader${acvers}
diff --git a/configure.ac b/configure.ac
index 0d33da2c26eefa04b391b3fc9c42a3471b2acbab..f0ab68d72d114554dac355f2623c83ad7dafd1c0 100644
--- a/configure.ac
+++ b/configure.ac
@@ -3,7 +3,7 @@ AC_PREREQ(2.54)
 AC_INIT([mpeg2dec],[0.5.0-svn],[])
 
 AC_CONFIG_SRCDIR([src/mpeg2dec.c])
-AC_CONFIG_AUX_DIR(autotools)
+AC_CONFIG_AUX_DIR(.auto)
 AC_CONFIG_FILES([Makefile include/Makefile test/Makefile
     doc/Makefile src/Makefile libmpeg2/Makefile libmpeg2/convert/Makefile
     libvo/Makefile vc++/Makefile
@@ -133,8 +133,8 @@ AC_PROG_LIBTOOL
 dnl Checks for libraries.
 
 dnl Checks for header files.
-INCLUDES='-I$(top_srcdir)/include -I$(top_builddir)/include'
-AC_SUBST([INCLUDES])
+AM_CPPFLAGS='-I$(top_srcdir)/include -I$(top_builddir)/include'
+AC_SUBST([AM_CPPFLAGS])
 AC_HEADER_TIME
 AC_CHECK_TYPES([struct timeval], [], [],
     [#include <sys/time.h>